geneSetPerm: Test gene set enrichment by permutating gene labels of...

In bedapub/ribiosGSEA: Gene-Set Enrichment Analysis Tools in Ribios

Test gene set enrichment by permutating gene labels of statistics

Description

Test gene set enrichment by permutating gene labels of statistics

Usage

geneSetPerm(stats, indList, Nsim = 9999)

Arguments

stats	Statistics
indList	a list of integers, indicating indices of genes of gene sets (index starts from 1, following R's convention)
Nsim	number of simulations

Value

A data frame containg mean statistic, gene set size, and p-values

See Also

geneSetTest, a R implementation in the limma package

Examples

set.seed(1887)
stats <- rnorm(1000)
gsList <- list(gs1=c(3,4,5), gs2=c(7,8,9))
geneSetPerm(stats, gsList, Nsim=99)
gsList2 <- list(gs1=c(3,4,5), gs2=c(7,8,9), gs3=integer())
geneSetPerm(stats, gsList2, Nsim=99)
gsList3 <- sample(1:1000, 200)
geneSetPerm(stats, gsList3, Nsim=99)

bedapub/ribiosGSEA documentation built on March 30, 2023, 3:26 p.m.