Alan Murphy
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/MungeSumstats |
| git_branch: RELEASE_3_16 |
| git_last_commit: 00916cd |
| git_last_commit_date: 2022-11-01 11:24:38 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:42 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the MungeSumstats package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MungeSumstats.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1309/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MungeSumstats 1.6.0 (landing page) Alan Murphy
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MungeSumstats |
| Version: 1.6.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MungeSumstats.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings MungeSumstats_1.6.0.tar.gz |
| StartedAt: 2023-04-11 03:48:20 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 03:57:13 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 532.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MungeSumstats.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MungeSumstats.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings MungeSumstats_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/MungeSumstats.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MungeSumstats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MungeSumstats' version '1.6.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'MungeSumstats' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_genome_builds 77.65 3.16 90.85
format_sumstats 45.13 1.75 54.71
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
MungeSumstats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL MungeSumstats ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'MungeSumstats' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MungeSumstats)
MungeSumstats.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(MungeSumstats)
>
> test_check("MungeSumstats")
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4057aa786e.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f407bea2399
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A0 A1 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4057aa786e.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.006 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4021be30ca.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f407bea2399
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4021be30ca.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Sorting coordinates.
Filtering SNPs based on INFO score.
46 SNPs are below the INFO threshold of 0.9 and will be removed.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF/info_filter.tsv.gz
INFO_filter==0. Skipping INFO score filtering step.
Filtering SNPs based on INFO score.
All rows have INFO>=0.9
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Sorting coordinates.
3 p-values are >1 which LDSC/MAGMA may not be able to handle. These will be converted to 1.
5 p-values are <0 which LDSC/MAGMA may not be able to handle. These will be converted to 0.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Sorting coordinates.
8 p-values are <=5e-324 which LDSC/MAGMA may not be able to handle. These will be converted to 0.
Reading header.
Tabular format detected.
Reading header.
Tabular format detected.
Reading header.
Tabular format detected.
Reading header.
VCF format detected.This will be converted to a standardised table format.
Importing tabular file: F:/biocbuild/bbs-3.16-bioc/R/library/MungeSumstats/extdata/eduAttainOkbay.txt
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Computing Z-score from P using formula: `sign(BETA)*sqrt(stats::qchisq(P,1,lower=FALSE)`
Standardising column headers.
First line of summary statistics file:
SNP CHR BP A1 A2 FRQ BETA SE P Z newZ
Computing Z-score from BETA ans SE using formula: `BETA/SE`
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40c214ef3.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4064f6775
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName EAF Beta SE Pval CHR_BP_A2_A1
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Column CHR_BP_A2_A1 has been separated into the columns CHR, BP, A2, A1
Standardising column headers.
First line of summary statistics file:
SNP FRQ BETA SE P CHR BP A2 A1
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40c214ef3.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f405f4e71d1.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4064f6775
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f405f4e71d1.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401a864db5.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4036be4520
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName EAF Beta SE Pval CHR_BP_A2_A1 CHR_BP_A2_A1_2
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Warning: Multiple columns in the sumstats file seem to relate to Chromosome:Base Pair position:A2:A1.
The column CHR_BP_A2_A1_2 will be kept whereas the column(s) CHR_BP_A2_A1 will be removed.
If this is not the correct column to keep, please remove all incorrect columns from those listed here before
running `format_sumstats()`.
Column CHR_BP_A2_A1_2 has been separated into the columns CHR, BP, A2, A1
Standardising column headers.
First line of summary statistics file:
SNP FRQ BETA SE P CHR BP A2 A1
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401a864db5.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f405e357b83.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4036be4520
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f405e357b83.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f403f9480a.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401b484a9
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS EAF Beta SE Pval alleles allele
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Warning: Multiple columns in the sumstats file seem to relate to alleles A1>A2.
The column ALLELES will be kept whereas the column(s) ALLELE will be removed.
If this is not the correct column to keep, please remove all incorrect columns from those listed here before
running `format_sumstats()`.
Column ALLELES has been separated into the columns A1, A2
Checking A1 is uppercase
Checking A2 is uppercase
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f403f9480a.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f406e47c8a.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401b484a9
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f406e47c8a.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.018 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40470f34d6.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401b593303
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName A1 A2 EAF Beta SE Pval CHR_BP
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Column CHR_BP has been separated into the columns CHR, BP
Standardising column headers.
First line of summary statistics file:
SNP A1 A2 FRQ BETA SE P CHR BP
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40470f34d6.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.002 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f405c851719.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401b593303
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f405c851719.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f402d86fe8.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f406fc222c6
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName A1 A2 EAF Beta SE Pval CHR_BP CHR_BP_2
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Warning: Multiple columns in the sumstats file seem to relate to Chromosome:Base Pair position.
The column CHR_BP_2 will be kept whereas the column(s) CHR_BP will be removed.
If this is not the correct column to keep, please remove all incorrect columns from those listed here before
running `format_sumstats()`.
Column CHR_BP_2 has been separated into the columns CHR, BP
Standardising column headers.
First line of summary statistics file:
SNP A1 A2 FRQ BETA SE P CHR BP
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f402d86fe8.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4059c367a9.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f406fc222c6
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4059c367a9.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f404ab2330.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4056211389
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f404ab2330.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4016806a03.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40590b100e
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4016806a03.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Setting sorted=FALSE (required when formatted=FALSE).
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4029852a0a.tsv.gz
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Assigning N=1000 for all SNPs.
N already exists within sumstats_dt.
[1] "Testing: compute_n='ldsc'"
Computing effective sample size using the LDSC method:
Neff = (N_CAS+N_CON) * (N_CAS/(N_CAS+N_CON)) / mean((N_CAS/(N_CAS+N_CON))[(N_CAS+N_CON)==max(N_CAS+N_CON)]))
[1] "Testing: compute_n='giant'"
Computing effective sample size using the GIANT method:
Neff = 2 / (1/N_CAS + 1/N_CON)
[1] "Testing: compute_n='metal'"
Computing effective sample size using the METAL method:
Neff = 4 / (1/N_CAS + 1/N_CON)
[1] "Testing: compute_n='sum'"
Computing sample size using the sum method:
N = N_CAS + N_CON
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4069d5965.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f407ee457ec
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4069d5965.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f407ae35f2d.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF
Saving output messages to:
F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF/MungeSumstats_log_msg.txt
Any runtime errors will be saved to:
F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF/MungeSumstats_log_output.txt
Messages will not be printed to terminal.
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4045b22ef8.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40fa4382b
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4045b22ef8.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4036827bf5.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f409981ab6
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 186 rows
- 93 unique variants
- 140 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
93 sumstat rows are duplicated. These duplicates will be removed.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4036827bf5.tsv.gz
Summary statistics report:
- 93 rows (50% of original 186 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40502e1739.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f409981ab6
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40502e1739.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4044394c2b.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f409981ab6
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 94 rows
- 94 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
1 base-pair positions are duplicated in the sumstats file. These duplicates will be removed.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Checking for bi-allelic SNPs.
Loading SNPlocs data.
Loading reference genome data.
Preprocessing RSIDs.
Validating RSIDs of 93 SNPs using BSgenome::snpsById...
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
BSgenome::snpsById done in 51 seconds.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4044394c2b.tsv.gz
Summary statistics report:
- 93 rows (98.9% of original 94 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.866 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4073aa302e.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40ea3f20
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Filtering effect columns, ensuring none equal 0.
5 SNPs have effect values = 0 and will be removed
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
44 SNPs (50%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4073aa302e.tsv.gz
Summary statistics report:
- 88 rows (94.6% of original 93 rows)
- 88 unique variants
- 65 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f405b7052a6.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4020bd3aa2
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval FRQ
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs based on FRQ.
38 SNPs are below the FRQ threshold of 0.9 and will be removed.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF/frq_filter.tsv.gz
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
55 SNPs (100%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f405b7052a6.tsv.gz
Summary statistics report:
- 55 rows (59.1% of original 93 rows)
- 55 unique variants
- 41 genome-wide significant variants (P<5e-8)
- 16 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 EAF BETA SE P FRQ
1: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10 1.863269
2: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14 1.169733
3: rs1008078 1 91189731 T C 0.37310 -0.016 0.003 6.005e-10 1.401423
4: rs61787263 1 98618714 T C 0.76120 0.016 0.003 5.391e-08 1.873332
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4059473ead.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4020bd3aa2
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval FRQ
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs based on FRQ.
38 SNPs are below the FRQ threshold of 0.9 and will be removed.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF/frq_filter.tsv.gz
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
55 SNPs (100%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=FALSE, the FRQ column will be renamed MAJOR_ALLELE_FRQ to differentiate the values from
minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4059473ead.tsv.gz
Summary statistics report:
- 55 rows (59.1% of original 93 rows)
- 55 unique variants
- 41 genome-wide significant variants (P<5e-8)
- 16 chromosomes
Done munging in 0.002 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 EAF BETA SE P
1: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
2: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
3: rs1008078 1 91189731 T C 0.37310 -0.016 0.003 6.005e-10
4: rs61787263 1 98618714 T C 0.76120 0.016 0.003 5.391e-08
MAJOR_ALLELE_FRQ
1: 1.863269
2: 1.169733
3: 1.401423
4: 1.873332
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4031a634e1.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40768c5d55
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
SNP CHR BP A1 A2 FRQ BETA SE P
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4031a634e1.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401335661f.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f408c42f0
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval INFO
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
Filtering SNPs based on INFO score.
38 SNPs are below the INFO threshold of 0.9 and will be removed.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF/info_filter.tsv.gz
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
28 SNPs (50.9%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401335661f.tsv.gz
Summary statistics report:
- 55 rows (59.1% of original 93 rows)
- 55 unique variants
- 41 genome-wide significant variants (P<5e-8)
- 16 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P INFO
1: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10 1.863269
2: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14 1.169733
3: rs1008078 1 91189731 T C 0.37310 -0.016 0.003 6.005e-10 1.401423
4: rs61787263 1 98618714 T C 0.76120 0.016 0.003 5.391e-08 1.873332
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401992a89.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f405f7411a8
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401992a89.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401b1643fb.tsv.gz
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401b1643fb.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
[1] "F:\\biocbuild\\bbs-3.16-bioc\\tmpdir\\Rtmps3NCGF/data/file1\\file20f40158c1f85.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.16-bioc\\tmpdir\\Rtmps3NCGF/data/file2\\file20f4034fd10f2.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.16-bioc\\tmpdir\\Rtmps3NCGF/data/file3\\file20f407b4b3a16.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.16-bioc\\tmpdir\\Rtmps3NCGF/data/file4\\file20f405e6b19a2.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.16-bioc\\tmpdir\\Rtmps3NCGF/data/file5\\file20f4020c21f93.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.16-bioc\\tmpdir\\Rtmps3NCGF/data/file6\\file20f403a2435b0.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.16-bioc\\tmpdir\\Rtmps3NCGF/data/file7\\file20f4035fb7cfe.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.16-bioc\\tmpdir\\Rtmps3NCGF/data/file8\\file20f4017956fd2.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.16-bioc\\tmpdir\\Rtmps3NCGF/data/file9\\file20f401de25564.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.16-bioc\\tmpdir\\Rtmps3NCGF/data/file10\\file20f404a2f1b13.tsv.gz"
10 file(s) found.
Parsing info from 10 log file(s).
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401f6030d4.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40699d8bd
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 92 unique variants
- 69 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
WARNING: 1 rows in sumstats file are missing data and will be removed.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
46 SNPs (50%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401f6030d4.tsv.gz
Summary statistics report:
- 92 rows (98.9% of original 93 rows)
- 92 unique variants
- 69 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs10061788 5 87934707 A G 0.2164 0.021 0.004 2.464e-09
2: rs1007883 16 51163406 T C 0.3713 -0.015 0.003 5.326e-08
3: rs1008078 1 91189731 T C 0.3731 -0.016 0.003 6.005e-10
4: rs1043209 14 23373986 A G 0.6026 0.018 0.003 1.816e-11
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4077f010e8.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40699d8bd
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4077f010e8.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs10061788 5 87934707 A G 0.2164 0.021 0.004 2.464e-09
2: rs1007883 16 51163406 T C 0.3713 -0.015 0.003 5.326e-08
3: rs1008078 1 91189731 T C 0.3731 -0.016 0.003 6.005e-10
4: rs1043209 14 23373986 A G 0.6026 0.018 0.003 1.816e-11
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f403e66274e.tsv.gz
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 21 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Loading SNPlocs data.
There is no Chromosome or Base Pair Position column found within the data. It must be inferred from other column information.
Loading reference genome data.
Preprocessing RSIDs.
Validating RSIDs of 1 SNPs using BSgenome::snpsById...
BSgenome::snpsById done in 1 seconds.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f403e66274e.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.03 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs10061788 5 87934707 A G 0.2164 0.021 0.004 2.464e-09
2: rs1007883 16 51163406 T C 0.3713 -0.015 0.003 5.326e-08
3: rs1008078 1 91189731 T C 0.3731 -0.016 0.003 6.005e-10
4: rs1043209 14 23373986 A G 0.6026 0.018 0.003 1.816e-11
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401b051ba9.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4074e71c5f
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
chromosome rs_id markername position_hg18 Effect_allele Other_allele EAF_HapMapCEU N_SMK Effect_SMK StdErr_SMK P_value_SMK N_NONSMK Effect_NonSMK StdErr_NonSMK P_value_NonSMK
Summary statistics report:
- 5 rows
- 5 unique variants
- 1 chromosomes
Checking for multi-GWAS.
WARNING: Multiple traits found in sumstats file only one of which can be analysed:
SMK, NONSMK
Standardising column headers.
First line of summary statistics file:
CHR SNP MARKERNAME POSITION_HG18 A2 A1 EAF_HAPMAPCEU N EFFECT STDERR P_VALUE N_NONSMK EFFECT_NONSMK STDERR_NONSMK P_VALUE_NONSMK
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
1 SNP IDs are not correctly formatted and will be removed.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Column MARKERNAME has been separated into the columns CHR, BP
Standardising column headers.
First line of summary statistics file:
CHR SNP POSITION_HG18 A2 A1 EAF_HAPMAPCEU N BETA SE P N_NONSMK EFFECT_NONSMK STDERR_NONSMK P_VALUE_NONSMK BP
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Ensuring that the N column is all integers.
The sumstats N column is not all integers, this could effect downstream analysis. These will be converted to integers.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Making X/Y/MT CHR uppercase.
N already exists within sumstats_dt.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401b051ba9.tsv.gz
Summary statistics report:
- 4 rows (80% of original 5 rows)
- 4 unique variants
- 0 genome-wide significant variants (P<5e-8)
- 1 chromosomes
Done munging in 0.002 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 POSITION_HG18 EAF_HAPMAPCEU N BETA
1: rs1000050 chr1 161003087 C T 161003087 0.9000 36257 0.0001
2: rs1000073 chr1 155522020 G A 155522020 0.3136 36335 0.0046
3: rs1000075 chr1 94939420 C T 94939420 0.3583 38959 -0.0013
4: rs1000085 chr1 66630503 G C 66630503 0.1667 38761 0.0053
SE P N_NONSMK EFFECT_NONSMK STDERR_NONSMK P_VALUE_NONSMK
1: 0.0109 0.9931 127514 0.0058 0.0059 0.3307
2: 0.0083 0.5812 126780 0.0038 0.0045 0.3979
3: 0.0082 0.8687 147567 -0.0043 0.0044 0.3259
4: 0.0095 0.5746 147259 -0.0034 0.0052 0.5157
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40286f4b2.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4021aa5595
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval N N_fixed
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Ensuring that the N column is all integers.
The sumstats N column is not all integers, this could effect downstream analysis. These will be converted to integers.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
N already exists within sumstats_dt.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40286f4b2.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P N N_FIXED
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08 5 5
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10 1 1
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14 1 1
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08 7 7
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f403d564d92.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f405ca622b7
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval N
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
The sumstats N column is not all integers, this could effect downstream analysis.These will NOT be converted to integers.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
1 SNPs have N values 5 standard deviations above the mean and will be removed
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF/n_large.tsv.gz
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
N already exists within sumstats_dt.
47 SNPs (51.1%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f403d564d92.tsv.gz
Summary statistics report:
- 92 rows (98.9% of original 93 rows)
- 92 unique variants
- 69 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P N
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08 3
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10 5
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14 3
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08 3
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401c784c83.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f405ca622b7
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval N
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
The sumstats N column is not all integers, this could effect downstream analysis.These will NOT be converted to integers.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
1 SNPs have N values 5 standard deviations above the mean and will be removed
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF/n_large.tsv.gz
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
N already exists within sumstats_dt.
47 SNPs (51.1%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401c784c83.tsv.gz
Summary statistics report:
- 92 rows (98.9% of original 93 rows)
- 92 unique variants
- 69 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P N
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08 3
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10 5
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14 3
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08 3
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40c61921.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f405ca622b7
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval N
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
The sumstats N column is not all integers, this could effect downstream analysis.These will NOT be converted to integers.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
1 SNPs have N values 5 standard deviations above the mean and will be removed
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF/n_large.tsv.gz
Removing rows where is.na(N)
0 SNPs have N values that are NA and will be removed.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF/n_null.tsv.gz
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
N already exists within sumstats_dt.
47 SNPs (51.1%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40c61921.tsv.gz
Summary statistics report:
- 92 rows (98.9% of original 93 rows)
- 92 unique variants
- 69 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P N
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08 3
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10 5
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14 3
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08 3
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4059b13b13.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40619422e7
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 23 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
3 SNPs are on chromosomes X, Y, MT and will be removed
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF/chr_excl.tsv.gz
Warning: When method is an integer, must be >0.
45 SNPs (50%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4059b13b13.tsv.gz
Summary statistics report:
- 90 rows (96.8% of original 93 rows)
- 90 unique variants
- 67 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f402d2c3979.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40619422e7
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f402d2c3979.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40510747fb
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
SNP CHR BP A1 A2 FRQ BETA SE P
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f404ef63502
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
SNP CHR BP A1 A2 FRQ BETA SE P
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4056a7bf4.vcf.bgz
Sorting coordinates.
Converting summary statistics to Genomic Ranges.
Converting summary statistics to VRanges.
Writing in VCF format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4056a7bf4.vcf.bgz
Loading required namespace: GenomicFiles
Using local VCF.
Finding empty VCF columns based on first 10,000 rows.
1 sample detected: GWAS
Constructing ScanVcfParam object.
Reading VCF file: single-threaded
Converting VCF to data.table.
Expanding VCF first, so number of rows may increase.
Checking for empty columns.
Time difference of 0.1 secs
VCF data.table contains: 93 rows x 11 columns.
Time difference of 0.6 secs
No INFO (SI) column detected.
Standardising column headers.
First line of summary statistics file:
ID chr BP end REF ALT SNP FRQ BETA SE P
Using local VCF.
bgzip-compressing VCF file.
Finding empty VCF columns based on first 10,000 rows.
Dropping 1 duplicate column(s).
1 sample detected: EBI-a-GCST005647
Constructing ScanVcfParam object.
VCF contains: 39,630,630 variant(s) x 1 sample(s)
Reading VCF file: single-threaded
Converting VCF to data.table.
Expanding VCF first, so number of rows may increase.
Dropping 1 duplicate column(s).
Checking for empty columns.
Unlisting 3 columns.
Dropped 314 duplicate rows.
Time difference of 0.1 secs
VCF data.table contains: 101 rows x 11 columns.
Time difference of 0.6 secs
Renaming ID as SNP.
VCF file has -log10 P-values; these will be converted to unadjusted p-values in the 'P' column.
No INFO (SI) column detected.
Standardising column headers.
First line of summary statistics file:
SNP chr BP end REF ALT FILTER AF ES LP SE P
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401235c79.vcf.bgz
Sorting coordinates.
Converting summary statistics to Genomic Ranges.
Converting summary statistics to VRanges.
Writing in VCF format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401235c79.vcf.bgz
Using local VCF.
Finding empty VCF columns based on first 10,000 rows.
1 sample detected: GWAS
Constructing ScanVcfParam object.
Reading VCF file: single-threaded
Converting VCF to data.table.
Expanding VCF first, so number of rows may increase.
Checking for empty columns.
Time difference of 0.1 secs
VCF data.table contains: 101 rows x 13 columns.
Time difference of 0.4 secs
VCF file has -log10 P-values; these will be converted to unadjusted p-values in the 'P' column.
No INFO (SI) column detected.
Standardising column headers.
First line of summary statistics file:
ID chr BP end REF SNP END FILTER FRQ BETA LP SE P
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f409f342a.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF
Standardising column headers.
First line of summary statistics file:
SNP P FRQ BETA CHR BP
Summary statistics report:
- 5 rows
- 5 unique variants
- 0 genome-wide significant variants (P<5e-8)
- 1 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
5 SNP IDs contain other information in the same column. These will be separated.
Checking for merged allele column.
Column SNP_INFO has been separated into the columns A1, A2
Checking A1 is uppercase
Checking A2 is uppercase
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
SE is not present but can be imputed with BETA & P. Set impute_se=TRUE and rerun to do this.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
3 SNPs (60%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f409f342a.tsv.gz
Summary statistics report:
- 5 rows (100% of original 5 rows)
- 5 unique variants
- 0 genome-wide significant variants (P<5e-8)
- 1 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 P FRQ BETA
1: rs140052487 1 54353 C A 0.037219838 0.3000548 0.8797957
2: rs558796213 1 54564 G T 0.004382482 0.5848666 0.7068747
3: rs561234294 1 54591 A G 0.070968402 0.3334671 0.7319726
4: rs2462492 1 54676 C T 0.065769040 0.6220120 0.9316344
Returning data directly.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401bf0306e.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF
Standardising column headers.
First line of summary statistics file:
SNP P FRQ BETA CHR BP A1 A2
Summary statistics report:
- 5 rows
- 5 unique variants
- 0 genome-wide significant variants (P<5e-8)
- 1 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
SE is not present but can be imputed with BETA & P. Set impute_se=TRUE and rerun to do this.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
3 SNPs (60%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401bf0306e.tsv.gz
Summary statistics report:
- 5 rows (100% of original 5 rows)
- 5 unique variants
- 0 genome-wide significant variants (P<5e-8)
- 1 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 P FRQ BETA
1: rs140052487 1 54353 C A 0.037219838 0.3000548 0.8797957
2: rs558796213 1 54564 G T 0.004382482 0.5848666 0.7068747
3: rs561234294 1 54591 A G 0.070968402 0.3334671 0.7319726
4: rs2462492 1 54676 C T 0.065769040 0.6220120 0.9316344
Returning data directly.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40f2e12ba.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4043c92fb8
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4039156a77.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f402258325c
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4039156a77.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f407dc0111b.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f402258325c
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f407dc0111b.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f404f3455dc.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4071802225
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f404f3455dc.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40149641f4.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f407c0f62c3
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40149641f4.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401d9d5445.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f406cbc7e9c
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
5 SNPs have SE values <= 0 and will be removed
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
44 SNPs (50%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401d9d5445.tsv.gz
Summary statistics report:
- 88 rows (94.6% of original 93 rows)
- 88 unique variants
- 65 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval Support
Returning unmapped column names without making them uppercase.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval Support
Returning unmapped column names without making them uppercase.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4077a549b1.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401fe67cb7.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40b3b69ca
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y/MT CHR uppercase.
Warning: When method is an integer, must be >0.
Sorting coordinates.
Writing in tabular format ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401fe67cb7.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.001 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 EAF BETA SE P
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning data directly.
Converting summary statistics to Genomic Ranges.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f407826271c.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f404f805da5.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40624a4e57.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f405991bf7.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4057175f52.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f405dab16a0.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4011274907.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40335b7720.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f402d7a78a8.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4031c168c8.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f401f6bd9b.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f4020e2ec3.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmps3NCGF\file20f40632f5cd7
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE
Summary statistics report:
- 93 rows
- 93 unique variants
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 135 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 135 ]
>
> proc.time()
user system elapsed
75.42 3.18 85.32
MungeSumstats.Rcheck/MungeSumstats-Ex.timings
| name | user | system | elapsed | |
| compute_nsize | 0.03 | 0.00 | 0.03 | |
| download_vcf | 0 | 0 | 0 | |
| find_sumstats | 0 | 0 | 0 | |
| format_sumstats | 45.13 | 1.75 | 54.71 | |
| formatted_example | 0.05 | 0.00 | 0.05 | |
| get_genome_builds | 77.65 | 3.16 | 90.85 | |
| import_sumstats | 0 | 0 | 0 | |
| index_tabular | 0.05 | 0.01 | 0.07 | |
| index_vcf | 0.05 | 0.00 | 0.05 | |
| liftover | 0.95 | 0.08 | 2.53 | |
| list_sumstats | 0 | 0 | 0 | |
| load_snp_loc_data | 0 | 0 | 0 | |
| parse_logs | 0.01 | 0.00 | 0.01 | |
| read_header | 0.00 | 0.02 | 0.02 | |
| read_sumstats | 0.02 | 0.00 | 0.01 | |
| read_vcf | 1.75 | 0.05 | 1.83 | |
| standardise_header | 0.02 | 0.00 | 0.05 | |
| vcf2df | 0.57 | 0.00 | 0.59 | |
| write_sumstats | 0.02 | 0.00 | 0.02 | |