getPvalues {topGO} | R Documentation

## 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.

### Author(s)

Adrian Alexa

### 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)

[Package topGO version 2.40.0 Index]