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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 (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("cpvSNP")

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

Documentation

Reference Manual PDF

Details

biocViews GeneSetEnrichment, Genetics, GenomicVariation, Pathways, Software, StatisticalMethod
Version 1.35.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License Artistic-2.0
Depends R (>= 2.10), GenomicFeatures, GSEABase(>= 1.24.0)
Imports methods, corpcor, BiocParallel, ggplot2, plyr
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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
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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/
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