nethet (version 1.4.2)

gsea.iriz: Irizarry approach for gene-set testing

Description

Irizarry approach for gene-set testing

Usage

gsea.iriz(x1, x2, gene.sets, gene.names, gs.names = NULL,
  method.p.adjust = "fdr", alternative = "two-sided")

Arguments

x1

Expression matrix (condition 1)

x2

Expression matrix (condition 2)

gene.sets

List of gene-sets

gene.names

Gene names

gs.names

Gene-set names

method.p.adjust

Method for p-value adjustment (default='fdr')

alternative

Default='two-sided' (uses two-sided p-values).

Value

• List consisting of
• pval.shift
  p-values measuring shift
• pval.scale
  p-values measuring scale
• pval.combined
  combined p-values (minimum of pval.shift and pval.scale)

Details

Implements the approach described in "Gene set enrichment analysis made simple" by Irizarry et al (2011). It tests for shift and/or change in scale of the distribution.

Examples

n <- 100
p <- 20
x1 <- matrix(rnorm(n*p),n,p)
x2 <- matrix(rnorm(n*p),n,p)
gene.names <- paste('G',1:p,sep='')
gsets <- split(gene.names,rep(1:4,each=5))
fit <- gsea.iriz(x1,x2,gsets,gene.names)
fit$pvals.combined

x2[,1:3] <- x2[,1:3]+0.5#variables 1-3 of first gene-set are upregulated
fit <- gsea.iriz(x1,x2,gsets,gene.names)
fit$pvals.combined