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Format Input Signatures from MSigDB

Source: R/format_msigdb.R
format_msigdb.Rd

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)
#> [1] "HALLMARK_TNFA_SIGNALING_VIA_NFKB" "HALLMARK_P53_PATHWAY"            
sig_list[[1]]
#> [1] "TNF"   "NFKB1" "NFKB2"