Read GMT file

Read GMT file

Usage

ParseGMT(gmtfile, swap_name_desc_if_needed = TRUE)

Arguments

gmtfile

Path to the GMT file

swap_name_desc_if_needed

Logical, whether to swap name and description fields. They will be swapped only if:

• swap_name_desc_if_needed is TRUE; and

• The descriptions are not empty; and

• The descriptions are shorter than the names; and

• The descriptions are not ID-like (i.e., hsa00001, or 123456).

Value

A list of gene sets, the names of the list are the gene set names, and each element is a vector of gene names.

Examples

# \donttest{
if (FALSE) {
# Example GMT file content
gmtfile <- system.file("extdata", "KEGG_2021_Human.gmt", package = "enrichit")
# Read the GMT file
ParseGMT(gmtfile)
}
# }