Alan Murphy
| Snapshot Date: 2023-07-11 14:00:14 -0400 (Tue, 11 Jul 2023) |
| git_url: https://git.bioconductor.org/packages/EWCE |
| git_branch: RELEASE_3_17 |
| git_last_commit: 9caffb0 |
| git_last_commit_date: 2023-05-22 12:38:19 -0400 (Mon, 22 May 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-07-12 11:57:29 -0400 (Wed, 12 Jul 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4616 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4379 |
| 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 | ||||
| Package 663/2229 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EWCE 1.8.2 (landing page) Alan Murphy
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
|
To the developers/maintainers of the EWCE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EWCE.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: EWCE |
| Version: 1.8.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EWCE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EWCE_1.8.2.tar.gz |
| StartedAt: 2023-07-12 01:35:59 -0400 (Wed, 12 Jul 2023) |
| EndedAt: 2023-07-12 02:10:21 -0400 (Wed, 12 Jul 2023) |
| EllapsedTime: 2061.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: EWCE.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EWCE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EWCE_1.8.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/EWCE.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EWCE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EWCE’ version ‘1.8.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘EWCE’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
generate_bootstrap_plots 44.627 0.881 60.697
controlled_geneset_enrichment 41.639 1.851 63.709
merged_ewce 30.108 1.152 43.494
generate_bootstrap_plots_for_transcriptome 28.149 1.069 39.545
filter_nonorthologs 24.944 0.739 34.690
filter_genes_without_1to1_homolog 24.106 0.673 35.003
bootstrap_enrichment_test 19.270 0.652 26.019
ewce_expression_data 18.640 0.907 28.063
check_ewce_genelist_inputs 16.750 0.517 23.524
sct_normalize 15.653 0.441 22.086
add_res_to_merging_list 14.083 1.532 20.169
filter_ctd_genes 13.529 0.369 20.330
merge_ctd 12.265 0.616 17.740
standardise_ctd 12.503 0.324 16.872
merge_sce 9.543 0.342 13.711
fix_bad_mgi_symbols 8.548 0.594 13.559
ctd_to_sce 8.485 0.311 13.703
bin_specificity_into_quantiles 8.386 0.298 11.174
bin_columns_into_quantiles 8.331 0.283 11.091
plot_ctd 8.116 0.201 11.093
drop_uninformative_genes 6.084 0.821 10.751
generate_celltype_data 6.593 0.256 9.176
get_celltype_table 5.116 0.245 7.002
merge_two_expfiles 4.856 0.277 7.015
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
4. └─ExperimentHub (local) .local(x, i, j = j, ...)
5. ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
6. │ └─base::eval(call, callEnv)
7. │ └─base::eval(call, callEnv)
8. └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
9. └─AnnotationHub (local) .local(x, i, j = j, ...)
10. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─value[[3L]](cond)
[ FAIL 3 | WARN 38 | SKIP 0 | PASS 111 ]
Error: Test failures
Execution halted
* 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: 1 ERROR
See
‘/Users/biocbuild/bbs-3.17-bioc/meat/EWCE.Rcheck/00check.log’
for details.
EWCE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EWCE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘EWCE’ ... ** using staged installation ** R ** 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 (EWCE)
EWCE.Rcheck/tests/testthat.Rout.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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(EWCE)
Loading required package: RNOmni
>
> test_check("EWCE")
1 core(s) assigned as workers (23 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Loading required namespace: ggdendro
+ Saving results ==> /tmp/RtmpZ139BU/ctd_testthat.rda
1 core(s) assigned as workers (23 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> /tmp/RtmpZ139BU/ctd_testthat.rda
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 core(s) assigned as workers (23 reserved).
Converting to sparse matrix.
Converting to sparse matrix.
1 core(s) assigned as workers (23 reserved).
Processing block [[1/5, 1/1]] ... OK
Processing block [[2/5, 1/1]] ... OK
Processing block [[3/5, 1/1]] ... OK
Processing block [[4/5, 1/1]] ... OK
Processing block [[5/5, 1/1]] ... OK
Processing block [[1/5, 1/1]] ... OK
Processing block [[2/5, 1/1]] ... OK
Processing block [[3/5, 1/1]] ... OK
Processing block [[4/5, 1/1]] ... OK
Processing block [[5/5, 1/1]] ... OK
Loading required namespace: sctransform
Converting to sparse matrix.
Calculating cell attributes from input UMI matrix: log_umi
Variance stabilizing transformation of count matrix of size 17757 by 3005
Model formula is y ~ log_umi
Get Negative Binomial regression parameters per gene
Using 2000 genes, 3005 cells
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Found 12 outliers - those will be ignored in fitting/regularization step
Second step: Get residuals using fitted parameters for 17757 genes
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Calculating gene attributes
Wall clock passed: Time difference of 1.612141 mins
Computing corrected UMI count matrix
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see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
+ <2 non-zero quantile bins detected in column. Assigning these values to default quantile ( 20 )
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 core(s) assigned as workers (23 reserved).
Generating gene background for mouse x human ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
=========== REPORT SUMMARY ===========
19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
16,482 intersect background genes used.
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
17 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
2 significant cell type enrichment results @ q<0.05 :
CellType annotLevel p fold_change sd_from_mean q
1 microglia 1 0 1.820518 2.409647 0
2 astrocytes_ependymal 1 0 1.357308 1.995351 0
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Generating gene background for mouse x human ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
=========== REPORT SUMMARY ===========
19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
16,482 intersect background genes used.
Standardising sct_data.
Aligning celltype names with standardise_ctd format.
Checking gene list inputs.
2 celltype(s) remain @ <= 0.05
Resampling random genes.
Computing gene scores.
Generating bootstrap plot for 2 celltype(s).
Saving plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_noText____VignetteGraphs.pdf
Saving plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtgene____VignetteGraphs.pdf
Saving plot --> /tmp/RtmpZ139BU/BootstrapPlots/bootDists____VignetteGraphs.pdf
Saving plot --> /tmp/RtmpZ139BU/BootstrapPlots/bootDists_LOG____VignetteGraphs.pdf
$plot1
$plot2
$plot3
$plot4
Warning: genelistSpecies not provided. Setting to 'human' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
15,259 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Returning gene_map as dictionary
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
2,016 / 15,259 (13%)
Total genes remaining after convert_orthologs :
13,243 / 15,259 (87%)
Generating gene background for mouse x human ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
=========== REPORT SUMMARY ===========
19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
16,482 intersect background genes used.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
Returning 19,129 unique genes from entire human genome.
Using intersect between background gene lists: 16,482 genes.
Standardising sct_data.
Using 1st column of tt as gene column: HGNC.symbol
1 core(s) assigned as workers (23 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
6 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
1 significant cell type enrichment results @ q<0.05 :
CellType annotLevel p fold_change sd_from_mean q
1 endothelial_mural 1 0 1.960864 4.367242 0
1 core(s) assigned as workers (23 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
5 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
2 significant cell type enrichment results @ q<0.05 :
CellType annotLevel p fold_change sd_from_mean q
1 interneurons 1 0 1.742023 3.948853 0
2 pyramidal_SS 1 0 1.991393 3.203248 0
Warning: genelistSpecies not provided. Setting to 'human' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Aligning celltype names with standardise_ctd format.
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
15,259 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Returning gene_map as dictionary
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
2,016 / 15,259 (13%)
Total genes remaining after convert_orthologs :
13,243 / 15,259 (87%)
Generating gene background for mouse x human ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
=========== REPORT SUMMARY ===========
19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
16,482 intersect background genes used.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
Returning 19,129 unique genes from entire human genome.
Using intersect between background gene lists: 16,482 genes.
Standardising sct_data.
Using 1st column of tt as gene column: HGNC.symbol
Generating exp data for bootstrap genes.
Converting data for bootstrap tests to sparse matrices.
endothelial_mural : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____endothelial_mural.pdf
endothelial_mural : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____endothelial_mural.pdf
endothelial_mural : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____endothelial_mural.pdf
$plot1
$plot2
microglia : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____microglia.pdf
microglia : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____microglia.pdf
microglia : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____microglia.pdf
$plot1
$plot2
oligodendrocytes : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____oligodendrocytes.pdf
oligodendrocytes : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____oligodendrocytes.pdf
oligodendrocytes : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____oligodendrocytes.pdf
$plot1
$plot2
interneurons : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____interneurons.pdf
interneurons : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____interneurons.pdf
interneurons : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____interneurons.pdf
$plot1
$plot2
astrocytes_ependymal : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____astrocytes_ependymal.pdf
astrocytes_ependymal : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____astrocytes_ependymal.pdf
astrocytes_ependymal : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____astrocytes_ependymal.pdf
$plot1
$plot2
pyramidal_CA1 : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____pyramidal_CA1.pdf
pyramidal_CA1 : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____pyramidal_CA1.pdf
pyramidal_CA1 : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____pyramidal_CA1.pdf
$plot1
$plot2
pyramidal_SS : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____pyramidal_SS.pdf
pyramidal_SS : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____pyramidal_SS.pdf
pyramidal_SS : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____pyramidal_SS.pdf
$plot1
$plot2
Generating exp data for bootstrap genes.
Converting data for bootstrap tests to sparse matrices.
interneurons : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____interneurons.pdf
interneurons : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____interneurons.pdf
interneurons : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____interneurons.pdf
$plot1
$plot2
pyramidal_SS : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____pyramidal_SS.pdf
pyramidal_SS : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____pyramidal_SS.pdf
pyramidal_SS : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____pyramidal_SS.pdf
$plot1
$plot2
pyramidal_CA1 : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____pyramidal_CA1.pdf
pyramidal_CA1 : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____pyramidal_CA1.pdf
pyramidal_CA1 : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____pyramidal_CA1.pdf
$plot1
$plot2
oligodendrocytes : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____oligodendrocytes.pdf
oligodendrocytes : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____oligodendrocytes.pdf
oligodendrocytes : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____oligodendrocytes.pdf
$plot1
$plot2
microglia : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____microglia.pdf
microglia : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____microglia.pdf
microglia : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____microglia.pdf
$plot1
$plot2
endothelial_mural : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____endothelial_mural.pdf
endothelial_mural : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____endothelial_mural.pdf
endothelial_mural : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____endothelial_mural.pdf
$plot1
$plot2
astrocytes_ependymal : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____astrocytes_ependymal.pdf
astrocytes_ependymal : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____astrocytes_ependymal.pdf
astrocytes_ependymal : Saving bootstrap plot --> /tmp/RtmpZ139BU/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____astrocytes_ependymal.pdf
$plot1
$plot2
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
Loading precomputed example bootstrap results.
Aligning celltype names with standardise_ctd format.
7 signficiant enrichment results @ bonferroni < 0.05
14.3% of hits are of the target cell type.
see ?ewceData and browseVignettes('ewceData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
require("SpatialExperiment")
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
Warning: genelistSpecies not provided. Setting to 'human' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
15,259 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Returning gene_map as dictionary
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
2,016 / 15,259 (13%)
Total genes remaining after convert_orthologs :
13,243 / 15,259 (87%)
Generating gene background for mouse x human ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
=========== REPORT SUMMARY ===========
19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
16,482 intersect background genes used.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
Returning 19,129 unique genes from entire human genome.
Using intersect between background gene lists: 16,482 genes.
Standardising sct_data.
Using 1st column of tt as gene column: HGNC.symbol
1 core(s) assigned as workers (23 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
28 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
1 significant cell type enrichment results @ q<0.05 :
CellType annotLevel p fold_change sd_from_mean q
1 endothelial_mural 1 0 1.628635 4.684982 0
1 core(s) assigned as workers (23 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
26 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
0 significant cell type enrichment results @ q<0.05 :
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Warning: genelistSpecies not provided. Setting to 'human' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
15,259 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Returning gene_map as dictionary
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
2,016 / 15,259 (13%)
Total genes remaining after convert_orthologs :
13,243 / 15,259 (87%)
Generating gene background for mouse x human ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
=========== REPORT SUMMARY ===========
19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
16,482 intersect background genes used.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
Returning 19,129 unique genes from entire human genome.
Using intersect between background gene lists: 16,482 genes.
Standardising sct_data.
Using 1st column of tt as gene column: HGNC.symbol
1 core(s) assigned as workers (23 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
10 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
0 significant cell type enrichment results @ q<0.05 :
1 core(s) assigned as workers (23 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
8 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
1 significant cell type enrichment results @ q<0.05 :
CellType annotLevel p fold_change sd_from_mean q
1 pyramidal_CA1 1 0 1.318978 1.682404 0
Warning: genelistSpecies not provided. Setting to 'human' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
15,259 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Returning gene_map as dictionary
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
2,016 / 15,259 (13%)
Total genes remaining after convert_orthologs :
13,243 / 15,259 (87%)
Generating gene background for mouse x human ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
=========== REPORT SUMMARY ===========
19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
16,482 intersect background genes used.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
Returning 19,129 unique genes from entire human genome.
Using intersect between background gene lists: 16,482 genes.
Standardising sct_data.
Using 1st column of tt as gene column: HGNC.symbol
1 core(s) assigned as workers (23 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
11 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
0 significant cell type enrichment results @ q<0.05 :
1 core(s) assigned as workers (23 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
9 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
0 significant cell type enrichment results @ q<0.05 :
Loading precomputed example bootstrap results.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Filtering CTD to 100 genes.
level: 1
Found 5 matrix types across 1 CTD levels.
- mean_exp
- median_exp
- specificity
- median_specificity
- specificity_quantiles
level: 2
Found 5 matrix types across 1 CTD levels.
- mean_exp
- median_exp
- specificity
- median_specificity
- specificity_quantiles
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Standardising CellTypeDataset
Found 5 matrix types across 2 CTD levels.
Processing level: 1
Processing level: 2
Filtering CTD to 100 genes.
level: level_1
Found 5 matrix types across 1 CTD levels.
- mean_exp
- median_exp
- specificity
- median_specificity
- specificity_quantiles
level: level_2
Found 5 matrix types across 1 CTD levels.
- mean_exp
- median_exp
- specificity
- median_specificity
- specificity_quantiles
see ?ewceData and browseVignettes('ewceData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
Check 1000Check 3005
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
1 core(s) assigned as workers (23 reserved).
Converting to sparse matrix.
Checking for non-expressed genes.
Checking for cells with no expressed genes.
DGE:: Limma...
248 / 1,000 genes dropped @ DGE adj_pval_thresh < 1e-05
Time difference of 1.256119 secs
1 core(s) assigned as workers (23 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> /tmp/RtmpZ139BU/ctd_kiCortexOnly.rda
+ Processing level 1 ...
Processing mean_exp
Processing specificity
Processing specificity_quantiles
+ Processing level 2 ...
Processing mean_exp
Processing specificity
Processing specificity_quantiles
No input_species provided. Setting to 'mouse'
+ Processing level 1 ...
Processing mean_exp
Processing specificity
Processing specificity_quantiles
+ Processing level 2 ...
Processing mean_exp
Processing specificity
Processing specificity_quantiles
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
trying URL 'http://www.informatics.jax.org/downloads/reports/MRK_List2.rpt'
Content type 'unknown' length 82692196 bytes (78.9 MB)
==================================================
downloaded 78.9 MB
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 rows do not have proper MGI symbols
Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 rows do not have proper MGI symbols
Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 rows do not have proper MGI symbols
Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
10 of 10 are not proper HGNC symbols.
Possible corruption of gene names by excel: Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
10 of 10 are not proper HGNC symbols.
Possible corruption of gene names by excel: Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
10 of 10 are not proper HGNC symbols.
Possible corruption of gene names by excel: Mar-01
Maps last updated on: Thu Oct 24 12:31:05 2019
Maps last updated on: Thu Oct 24 12:31:05 2019
9 of 10 gene symbols corrected.
1 of 10 gene symbols cannot be mapped.
Converting to sparse matrix.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 rows do not have proper MGI symbols
Tm4sf12
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 poorly annotated genes are replicates of existing genes. These are:
Tspan12
Converting to sparse matrix.
1 rows should have been corrected by checking synonyms.
0 rows STILL do not have proper MGI symbols.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
0 rows do not have proper MGI symbols
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
669 rows do not have proper MGI symbols
2310042E22Rik, BC005764, C130030K03Rik, Stmn1-rs1, Gm9846, E130309F12Rik, Fam211b, AI848285, Acpl2, 9630033F20Rik, Adrbk2, Syne1_loc2, Adc, Dlx1os, LOC106740, Pdxp, Atp6v0c-ps2, 2900056M20Rik, Epb4.1l1, A330050F15Rik
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
308 rows do not have proper MGI symbols
2310042E22Rik, BC005764, C130030K03Rik, Stmn1-rs1, Gm9846, E130309F12Rik, Fam211b, AI848285, Acpl2, 9630033F20Rik, Adrbk2, Syne1_loc2, Adc, Dlx1os, LOC106740, Pdxp, Atp6v0c-ps2, 2900056M20Rik, Epb4.1l1, A330050F15Rik
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 poorly annotated genes are replicates of existing genes. These are:
Hjurp
Converting to sparse matrix.
185 rows should have been corrected by checking synonyms.
126 rows STILL do not have proper MGI symbols.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
308 rows do not have proper MGI symbols
2310042E22Rik, BC005764, C130030K03Rik, Stmn1-rs1, Gm9846, E130309F12Rik, Fam211b, AI848285, Acpl2, 9630033F20Rik, Adrbk2, Syne1_loc2, Adc, Dlx1os, LOC106740, Pdxp, Atp6v0c-ps2, 2900056M20Rik, Epb4.1l1, A330050F15Rik
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 poorly annotated genes are replicates of existing genes. These are:
Hjurp
Converting to sparse matrix.
185 rows should have been corrected by checking synonyms.
126 rows STILL do not have proper MGI symbols.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 core(s) assigned as workers (23 reserved).
Preparing gene_df.
Dense matrix format detected.
Extracting genes from rownames.
100 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
91 genes extracted.
Extracting genes from ortholog_gene.
91 genes extracted.
Checking for genes without 1:1 orthologs.
Filtering gene_df with gene_map
Setting ortholog_gene to rownames.
Converting obj to sparseMatrix.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
9 / 100 (9%)
Total genes remaining after convert_orthologs :
91 / 100 (91%)
Converting to sparse matrix.
Converting to DelayedArray.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> /tmp/RtmpZ139BU/ctd_allKImouse.rda
+ Returning list of CTD file name, and the CTD itself.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Filtering by variance quantiles.
Converting to DelayedArray.
120 / 300 genes dropped @ DGE min_variance_quantile >= 5
Converting to sparse matrix.
Calculating cell attributes from input UMI matrix: log_umi
Variance stabilizing transformation of count matrix of size 300 by 3005
Model formula is y ~ log_umi
Get Negative Binomial regression parameters per gene
Using 300 genes, 3005 cells
|
| | 0%
|
|======================================================================| 100%
Found 2 outliers - those will be ignored in fitting/regularization step
Second step: Get residuals using fitted parameters for 300 genes
|
| | 0%
|
|======================================================================| 100%
Calculating gene attributes
Wall clock passed: Time difference of 14.82142 secs
Computing corrected UMI count matrix
|
| | 0%
|
|======================================================================| 100%
Filtering by variance quantiles.
Converting to DelayedArray.
120 / 300 genes dropped @ DGE min_variance_quantile >= 5
Filtering by variance quantiles.
Converting to DelayedArray.
120 / 300 genes dropped @ DGE min_variance_quantile >= 5
Filtering by variance quantiles.
Converting to DelayedArray.
/ Reading and realizing block 1/1 ... OK
\ Processing it ... OK
120 / 300 genes dropped @ DGE min_variance_quantile >= 5
Retrieving all organisms available in homologene.
Returning table with all species.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
+ CTD ==> SingleCellExperiment
Converting level: level_1
Returning all possible matrix names.
Converting level: level_2
Returning all possible matrix names.
The assay 'mean_exp' will be used to determine the proportion of zeroes for each batch.
Converting CTD to merged SCEs
ctd1
+ CTD ==> SingleCellExperiment
Converting level: level_1
Returning all possible matrix names.
Converting level: level_2
Returning all possible matrix names.
ctd2
+ CTD ==> SingleCellExperiment
Converting level: level_1
Returning all possible matrix names.
Converting level: level_2
Returning all possible matrix names.
Merging SCE at level: 1
[1] "ctd1"
[1] "15259 x 7"
[1] "ctd2"
[1] "15259 x 7"
The assay 'mean_exp' will be used to determine the proportion of zeroes for each batch.
Merging SCE at level: 2
[1] "ctd1"
[1] "15259 x 48"
[1] "ctd2"
[1] "15259 x 48"
The assay 'mean_exp' will be used to determine the proportion of zeroes for each batch.
[1] "level_1"
[1] "level_2"
Saving SCE_merged ==> /tmp/RtmpZ139BU/merged/CTD_SCE_merged.union.rds
+ Must set `as_SCE=TRUE` in order to merge CTD.
+ Returning merged CTD.
1 core(s) assigned as workers (23 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> /tmp/RtmpZ139BU/ctd_filec5cc6de6f014level_1.rda
+ Returning list of CTD file name, and the CTD itself.
1 core(s) assigned as workers (23 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> /tmp/RtmpZ139BU/ctd_filec5cc549be96alevel_2.rda
+ Returning list of CTD file name, and the CTD itself.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
0 non-overlapping gene(s) removed from exp1.
0 non-overlapping gene(s) removed from exp2.
19,972 intersecting genes remain.
Converting to data.frame
Converting to data.frame
Converting to sparse matrix.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
DGE:: Limma...
Loading required namespace: DESeq2
DGE:: DESeq2...
1 core(s) assigned as workers (23 reserved).
converting counts to integer mode
Note: levels of factors in the design contain characters other than
letters, numbers, '_' and '.'. It is recommended (but not required) to use
only letters, numbers, and delimiters '_' or '.', as these are safe characters
for column names in R. [This is a message, not a warning or an error]
estimating size factors
Note: levels of factors in the design contain characters other than
letters, numbers, '_' and '.'. It is recommended (but not required) to use
only letters, numbers, and delimiters '_' or '.', as these are safe characters
for column names in R. [This is a message, not a warning or an error]
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
Note: levels of factors in the design contain characters other than
letters, numbers, '_' and '.'. It is recommended (but not required) to use
only letters, numbers, and delimiters '_' or '.', as these are safe characters
for column names in R. [This is a message, not a warning or an error]
final dispersion estimates
fitting model and testing
Note: levels of factors in the design contain characters other than
letters, numbers, '_' and '.'. It is recommended (but not required) to use
only letters, numbers, and delimiters '_' or '.', as these are safe characters
for column names in R. [This is a message, not a warning or an error]
Loading required namespace: MAST
`fData` has no primerid. I'll make something up.
`cData` has no wellKey. I'll make something up.
[ FAIL 3 | WARN 38 | SKIP 0 | PASS 111 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-bootstrap_enrichment_test_2.R:10:9'): bootstrap enrichment function error handling and geneSizeControl runs as expected ──
Error: failed to load resource
name: EH5367
title: mouse_to_human_homologs
reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
▆
1. └─ewceData::mouse_to_human_homologs() at test-bootstrap_enrichment_test_2.R:10:8
2. ├─eh[["EH5367"]]
3. └─eh[["EH5367"]]
4. └─ExperimentHub (local) .local(x, i, j = j, ...)
5. ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
6. │ └─base::eval(call, callEnv)
7. │ └─base::eval(call, callEnv)
8. └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
9. └─AnnotationHub (local) .local(x, i, j = j, ...)
10. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─value[[3L]](cond)
── Error ('test-celltype_specificity_Aif1_Pvalb.R:7:9'): Cell type specificity Aif1, Pvalb ──
Error: failed to load resource
name: EH5381
title: cortex_mrna
reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
▆
1. └─ewceData::cortex_mrna() at test-celltype_specificity_Aif1_Pvalb.R:7:8
2. ├─eh[["EH5381"]]
3. └─eh[["EH5381"]]
4. └─ExperimentHub (local) .local(x, i, j = j, ...)
5. ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
6. │ └─base::eval(call, callEnv)
7. │ └─base::eval(call, callEnv)
8. └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
9. └─AnnotationHub (local) .local(x, i, j = j, ...)
10. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─value[[3L]](cond)
── Error ('test-controlled_geneset_enrichment.R:7:9'): Correct controlled & uncontrolled geneset enrichment calculations ──
Error: failed to load resource
name: EH5367
title: mouse_to_human_homologs
reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
▆
1. └─ewceData::mouse_to_human_homologs() at test-controlled_geneset_enrichment.R:7:8
2. ├─eh[["EH5367"]]
3. └─eh[["EH5367"]]
4. └─ExperimentHub (local) .local(x, i, j = j, ...)
5. ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
6. │ └─base::eval(call, callEnv)
7. │ └─base::eval(call, callEnv)
8. └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
9. └─AnnotationHub (local) .local(x, i, j = j, ...)
10. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─value[[3L]](cond)
[ FAIL 3 | WARN 38 | SKIP 0 | PASS 111 ]
Error: Test failures
Execution halted
EWCE.Rcheck/EWCE-Ex.timings
| name | user | system | elapsed | |
| add_res_to_merging_list | 14.083 | 1.532 | 20.169 | |
| bin_columns_into_quantiles | 8.331 | 0.283 | 11.091 | |
| bin_specificity_into_quantiles | 8.386 | 0.298 | 11.174 | |
| bootstrap_enrichment_test | 19.270 | 0.652 | 26.019 | |
| check_ewce_genelist_inputs | 16.750 | 0.517 | 23.524 | |
| check_percent_hits | 0.005 | 0.002 | 0.010 | |
| controlled_geneset_enrichment | 41.639 | 1.851 | 63.709 | |
| ctd_to_sce | 8.485 | 0.311 | 13.703 | |
| drop_uninformative_genes | 6.084 | 0.821 | 10.751 | |
| ewce_expression_data | 18.640 | 0.907 | 28.063 | |
| ewce_plot | 0.107 | 0.007 | 0.153 | |
| example_bootstrap_results | 0.002 | 0.001 | 0.004 | |
| example_transcriptome_results | 0.003 | 0.002 | 0.009 | |
| filter_ctd_genes | 13.529 | 0.369 | 20.330 | |
| filter_genes_without_1to1_homolog | 24.106 | 0.673 | 35.003 | |
| filter_nonorthologs | 24.944 | 0.739 | 34.690 | |
| fix_bad_hgnc_symbols | 1.786 | 0.140 | 2.731 | |
| fix_bad_mgi_symbols | 8.548 | 0.594 | 13.559 | |
| fix_celltype_names | 0 | 0 | 0 | |
| generate_bootstrap_plots | 44.627 | 0.881 | 60.697 | |
| generate_bootstrap_plots_for_transcriptome | 28.149 | 1.069 | 39.545 | |
| generate_celltype_data | 6.593 | 0.256 | 9.176 | |
| get_celltype_table | 5.116 | 0.245 | 7.002 | |
| list_species | 0.014 | 0.003 | 0.022 | |
| load_rdata | 0.001 | 0.006 | 0.009 | |
| merge_ctd | 12.265 | 0.616 | 17.740 | |
| merge_sce | 9.543 | 0.342 | 13.711 | |
| merge_two_expfiles | 4.856 | 0.277 | 7.015 | |
| merged_ewce | 30.108 | 1.152 | 43.494 | |
| plot_ctd | 8.116 | 0.201 | 11.093 | |
| sct_normalize | 15.653 | 0.441 | 22.086 | |
| standardise_ctd | 12.503 | 0.324 | 16.872 | |