gene2set {cogena} | R Documentation

## 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.v5.0.symbols.gmt.xz"
    annofile <- system.file("extdata", annoGMT, package="cogena")
    # the DEG gene-sets matrix
    anno <- gene2set(annofile, rownames(DEexprs))

[Package cogena version 1.14.0 Index]