write_gmt: Write GMT file

In mulea: Enrichment Analysis using Multiple Ontologies and False Discovery Rate

Write GMT file

Description

Writes gene set or ontology data.frame with specific formatting (columns representing ontology identifiers, descriptions, and associated lists of values) and writes it to a file in a standardized Gene Matrix Transposed (GMT) file format.

Usage

write_gmt(gmt, file)

Arguments

gmt	A data.frame containing the data to be written, imported from a GMT file with the read_gmt function.
file	Character, a path to a file.

Value

Returns the input as a GMT file at a specific location.

Examples

library(mulea)

# loading and filtering the example ontology from a GMT file
tf_gmt <- read_gmt(file = system.file(
    package="mulea", "extdata", 
    "Transcription_factor_RegulonDB_Escherichia_coli_GeneSymbol.gmt"))

# writing the filtered ontology to a GMT file

write_gmt(
    gmt = tf_gmt, 
    file = "Transcription_factor_RegulonDB_Escherichia_coli_GeneSymbol.gmt")

mulea documentation built on Sept. 30, 2024, 9:44 a.m.