filterGS: Filter by genes belonging to a gene set from a data frame

In tmod: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

Filter by genes belonging to a gene set from a data frame

Description

Filter a data frame or vector by genes belonging to a gene set

Usage

filterGS(genes, gs, mset = "all")

showModule(x, genes, gs, mset = "all", extra = NULL)

Arguments

genes	a character vector with gene IDs
gs	a character vector corresponding to the IDs of the gene sets to be shown
mset	Module set to use; see "tmodUtest" for details
x	a data frame or a vector
extra	no longer used.

Details

filterGS filters a vector of gene IDs based on whether the IDs belong to a given set of gene sets, returning a logical vector.

The showModule function is deprecated and will be removed in future.

Value

filterGS returns a logical vector of length equal to genes, with TRUE indicating that the given gene is a member of the gene sets in 'gs'.

Examples

data(Egambia)
## LI.M127 – type I interferon response
sel <- filterGS("LI.M127", Egambia$GENE_SYMBOL)
head(Egambia[sel, ])

tmod documentation built on March 31, 2023, 9 p.m.