PEI {cogena} | R Documentation

## 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)

[Package cogena version 1.28.0 Index]