gene2set: generate relationship between genes and gene-sets

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

generate relationship between genes and gene-sets

Description

Generate relationship between genes (gene SYMBOL) and gene-sets, such as Pathway or GO.

Usage

gene2set(annofile = NULL, genenames, TermFreq = 0)

annotationListToMatrix(annotation, genenames)

Arguments

annofile	a gmt file. Examples are from MSigDB Collections. A list of gene set could be find in the vignette of cogena
genenames	a SYMBOL gene names charactic vector.
TermFreq	a threshold for the Term Frequence. Default is zero.
annotation	a value returned by gmt2list.

Value

an gene and gene-set relationship matrix

Examples

data(Psoriasis)

#annotaion
annoGMT <- "c2.cp.kegg.v7.01.symbols.gmt.xz"
annofile <- system.file("extdata", annoGMT, package="cogena")
# the DEG gene-sets matrix
anno <- gene2set(annofile, rownames(DEexprs))

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