gsaPermute-package: Gene permutation procedure for unbiased gene set analyses.
In mooneymi/gsaPermute: Gene Permutation Procedure for Unbiased Gene Set Analysis

Description Details Author(s) See Also Examples

This package can be used to create random gene sets of approximately the same composition (same number of genes with the same number of SNPs) as an a priori defined gene set (e.g. from a publicly available pathway database). As part of a gene set (pathway) analysis, this procedure can be used to calculate a null distribution of association statistics for each pathway being tested, which enables adjustment of p-values for pathway size and linkage disequilibrium (correlation between SNPs).

Package:	gsaPermute
Type:	Package
Version:	1.0
Date:	2014-04-25
License:	GPLv3
Copyright:	(C) 2014 Michael Mooney

Michael Mooney

Maintainer: Michael Mooney <mooneymi@ohsu.edu>

makeRandomGS, snpsToGenes, getGeneSizes, getGeneSetComposition, makeGeneBins

data(sampleGSA)

# Get gene sizes, and bin genes by size
snpCounts = getGeneSizes(snpMap)
geneBins = makeGeneBins(snpCounts, 25)
  
# Get the composition of the target pathway
gsComp = getGeneSetComposition(snpCounts, pathways[[1]])

# Create random pathways (gene sets) that approximately match the composition of the target pathway
numPerms = 100
x = lapply(c(1:numPerms), function(x){gsComp})
names(x) = c(1:numPerms)
randomPathways = lapply(x, function(y){makeRandomGS(y, geneBins=geneBins)})