getPvalues {topGO} | R Documentation |
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])
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 |
~~ If necessary, more details than the description above ~~
An named vector of p-values is returned.
Adrian Alexa
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)