cpvSNP

DOI: 10.18129/B9.bioc.cpvSNP    

Gene set analysis methods for SNP association p-values that lie in genes in given gene sets

Bioconductor version: Release (3.13)

Gene set analysis methods exist to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. This package implements two such methods that require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs. Built-in plotting functions are available to help users visualize results.

Author: Caitlin McHugh, Jessica Larson, and Jason Hackney

Maintainer: Caitlin McHugh <mchughc at uw.edu>

Citation (from within R, enter citation("cpvSNP")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cpvSNP")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("cpvSNP")

 

PDF R Script Running gene set analyses with the "cpvSNP" package
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneSetEnrichment, Genetics, GenomicVariation, Pathways, Software, StatisticalMethod
Version 1.24.0
In Bioconductor since BioC 3.1 (R-3.2) (6.5 years)
License Artistic-2.0
Depends R (>= 2.10), GenomicFeatures, GSEABase(>= 1.24.0)
Imports methods, corpcor, BiocParallel, ggplot2, plyr
LinkingTo
Suggests TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package cpvSNP_1.24.0.tar.gz
Windows Binary cpvSNP_1.24.0.zip
macOS 10.13 (High Sierra) cpvSNP_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cpvSNP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cpvSNP
Package Short Url https://bioconductor.org/packages/cpvSNP/
Package Downloads Report Download Stats

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