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

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.

Package details

AuthorCaitlin McHugh, Jessica Larson, and Jason Hackney
Bioconductor views GeneSetEnrichment Genetics GenomicVariation Pathways StatisticalMethod
MaintainerCaitlin McHugh <mchughc@uw.edu>
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


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cpvSNP documentation built on Nov. 8, 2020, 6 p.m.