PEI: Significance of Gene sets enrichment.

In zhilongjia/cogena: co-expressed gene-set enrichment analysis

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.

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.

Value

a vector with P-values.

Examples

data(Psoriasis)
data(AllGeneSymbols)
annofile <- system.file("extdata", "c2.cp.kegg.v7.01.symbols.gmt.xz", package="cogena")
annoBG <- gene2set(annofile, AllGeneSymbols)
res <- PEI(rownames(DEexprs)[1:200], gene2set(annofile, rownames(DEexprs)[1:200]), annoBG)

zhilongjia/cogena documentation built on Nov. 21, 2023, 1:34 a.m.