getGenes {tmod}

Get genes belonging to a gene set

Description

Get genes belonging to a gene set

Usage

getGenes(gs = NULL, genes = NULL, fg = NULL, mset = "all", as.list = FALSE)

Arguments

gs

gene set IDs; if NULL, returns all genes from all gene sets

genes

character vector with gene IDs. If not NULL, only genes from this parameter will be considered.

fg

genes which are in the foreground set

mset

gene set to use (default: all tmod gene sets)

as.list

should a list of genes rather than a data frame be returned

Details

Create a data frame mapping each module to a comma separated list of genes. If genelist is provided, then only genes in that list will be shown. An optional column, "fg" informs which genes are in the "foreground" data set.

Value

data frame containing module to gene mapping, or a list (if as.list == TRUE