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 setsBioconductor version: Development (3.22)
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, entercitation("cpvSNP")): Installation
To install this package, start R (version "4.5") 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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cpvSNP")Follow Installation instructions to use this package in your R session.
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