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 (3.16)

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>

Installation

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

 

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	1.30.0
In Bioconductor since	BioC 3.1 (R-3.2) (8 years)
License	Artistic-2.0
Depends	R (>= 3.5.0), 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_1.30.0.tar.gz
Windows Binary	cpvSNP_1.30.0.zip
macOS Binary (x86_64)	cpvSNP_1.30.0.tgz
macOS Binary (arm64)	cpvSNP_1.30.0.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