gene2set: generate relationship between genes and gene-sets
In cogena: co-expressed gene-set enrichment analysis

Description Usage Arguments Value Examples

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

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

annotationListToMatrix(annotation, genenames)

`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`.

an gene and gene-set relationship matrix

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))