load_genesets_gmtfile: parse genesets in GMT format where gene identifiers are...

In goat: Gene Set Analysis Using the Gene Set Ordinal Association Test

parse genesets in GMT format where gene identifiers are numeric Entrez gene IDs

Description

parse genesets in GMT format where gene identifiers are numeric Entrez gene IDs

Usage

load_genesets_gmtfile(filename, label)

Arguments

filename

input file for this function should be the full path to genesets defined in GMT format

label

a shortname for the genesets in this file, for example "GO_CC", "KEGG", "MY_DB_V1". This will be stored in the 'source' column of the resulting table. Importantly, multiple testing correction in GOAT is grouped by this 'source' column so you probably want to use a different label for each collection-of-genesets that you load. Must not be empty, only allowed characters are; upper/lower-case letter, numbers 0-9 and underscore

Value

tibble with columns; source (character), source_version (character), id (character), name (character), genes (list), ngenes (int)

Example data;

URL: https://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp#C5 download this data: KEGG subset of curated pathways –>> NCBI (Entrez) Gene IDs filename should be something like "c2.cp.kegg.v2023.1.Hs.entrez.gmt"

Examples

  # TODO: update the filename to your downloaded file
  f = "C:/DATA/c2.cp.kegg.v2023.1.Hs.entrez.gmt"
  if(file.exists(f)) genesets_asis = load_genesets_gmtfile(f, label = "KEGG")

goat documentation built on April 3, 2025, 6:05 p.m.