cogena (version 1.6.2)

PEI: Significance of Gene sets enrichment.

Description

Caculating the significance of Gene sets enrichment based on the hypergeometric test. This function is mainly used internally.

Usage

PEI(genenames, annotation, annotationGenesPop)

Arguments

genenames

a vector of gene names.

annotation

data.frame with the gene (like all the differentially expressed genes) in row, gene set in column.

annotationGenesPop

data.frame with the gene in row, gene set in column. Here genes are genes in population with filering the non-nformative genes better.

Value

a vector with P-values.

Details

Here the genes in annotation can be a varity of types. like all the DEG, up-regualted genes or genes in a cluster. the gene names should be consistent with the genes in the gene sets.

Examples

data(Psoriasis)
data(AllGeneSymbols)
annofile <- system.file("extdata", "c2.cp.kegg.v5.0.symbols.gmt.xz", package="cogena")
annoBG <- gene2set(annofile, AllGeneSymbols)
res <- PEI(rownames(DEexprs)[1:200], gene2set(annofile, rownames(DEexprs)[1:200]), annoBG)