Bioconductor-mirror/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.

Getting started

Package details

AuthorCaitlin McHugh, Jessica Larson, and Jason Hackney
Bioconductor views GeneSetEnrichment Genetics GenomicVariation Pathways StatisticalMethod
MaintainerCaitlin McHugh <[email protected]>
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
Bioconductor-mirror/cpvSNP documentation built on June 1, 2017, 6:43 a.m.