topGO (version 2.24.0)

getPvalues: Convenient function to compute p-values from a gene expression matrix.

Description

Warping function of "mt.teststat", for computing p-values of a gene expression matrix.

Usage

getPvalues(edata, classlabel, test = "t", alternative = c("greater", "two.sided", "less")[1], genesID = NULL, correction = c("none", "Bonferroni", "Holm", "Hochberg", "SidakSS", "SidakSD", "BH", "BY")[8])

Arguments

edata

Gene expression matrix.

classlabel

The phenotype of the data

test

Which test statistic to use

alternative

The alternative of the test statistic

genesID

if a subset of genes is provided

correction

Multiple testing correction procedure

Value

An named numeric vector of p-values.

See Also

GOKSTest, groupStats-class, getSigGroups-methods

Examples

library(ALL)
data(ALL)

## discriminate B-cell from T-cell
classLabel <- as.integer(sapply(ALL$BT, function(x) return(substr(x, 1, 1) == 'T')))

## Differentially expressed genes
geneList <- getPvalues(exprs(ALL), classlabel = classLabel,
                       alternative = "greater", correction = "BY")

hist(geneList, 50)