gsea.iriz {nethet} | R Documentation

## 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).

### 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.

### 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)

### Author(s)

n.stadler

### 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

[Package nethet version 1.24.0 Index]