gene2set: generate relationship between genes and gene-sets

Description Usage Arguments Value Examples

View source: R/gene2set.R

Description

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

Usage

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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

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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))

cogena documentation built on Nov. 8, 2020, 6:54 p.m.