format_msigdb: Format Input Signatures from MSigDB

In IOBR: Immune Oncology Biological Research

Format Input Signatures from MSigDB

Description

Reads a GMT file from MSigDB and converts it into a named list of gene sets suitable for IOBR functions.

Usage

format_msigdb(gmt, ont = "term", gene = "gene")

Arguments

gmt	Character string. Path to a GMT file.
ont	Character string. Name of the signature/set column in the parsed GMT table. Default is '"term"'.
gene	Character string. Name of the gene column in the parsed GMT table. Default is '"gene"'.

Value

Named list of character vectors, where each element contains the genes belonging to one signature.

Examples

tf <- tempfile(fileext = ".gmt")
writeLines(
  c(
    "HALLMARK_TNFA_SIGNALING_VIA_NFKB\tNA\tTNF\tNFKB1\tNFKB2",
    "HALLMARK_P53_PATHWAY\tNA\tTP53\tMDM2\tCDKN1A"
  ),
  con = tf
)

sig_list <- format_msigdb(tf, ont = "term", gene = "gene")
names(sig_list)
sig_list[[1]]

IOBR documentation built on May 30, 2026, 5:07 p.m.