DOI: 10.18129/B9.bioc.cpvSNP    

This is the development version of cpvSNP; for the stable release version, see cpvSNP.

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

Bioconductor version: Development (3.15)

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")):


To install this package, start R (version "4.2") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


PDF   Reference Manual


biocViews GeneSetEnrichment, Genetics, GenomicVariation, Pathways, Software, StatisticalMethod
Version 1.27.0
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
Suggests TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle
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
Windows Binary
macOS 10.13 (High Sierra)
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

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: