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cpvSNP

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


Bioconductor version: Release (3.18)

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 "4.3") and enter:


if (!require("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")
Running gene set analyses with the "cpvSNP" package PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneSetEnrichment, Genetics, GenomicVariation, Pathways, Software, StatisticalMethod
Version 1.34.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License Artistic-2.0
Depends R (>= 3.5.0), GenomicFeatures, GSEABase(>= 1.24.0)
Imports methods, corpcor, BiocParallel, ggplot2, plyr
System Requirements
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Suggests TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle
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Package Archives

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

Source Package cpvSNP_1.34.0.tar.gz
Windows Binary cpvSNP_1.34.0.zip
macOS Binary (x86_64) cpvSNP_1.34.0.tgz
macOS Binary (arm64) cpvSNP_1.34.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cpvSNP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cpvSNP
Bioc Package Browser https://code.bioconductor.org/browse/cpvSNP/
Package Short Url https://bioconductor.org/packages/cpvSNP/
Package Downloads Report Download Stats