getPvalues {topGO}R Documentation

Function to compute p-values of a t-test for a gene expression matrix.

Description

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

Details

~~ If necessary, more details than the description above ~~

Value

An named vector of p-values is returned.

Author(s)

Adrian Alexa

See Also

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)

[Package topGO version 1.4.0 Index]