read_gmt: Read GMT File

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

Read GMT File

Description

Reads gene set or ontology data from a Gene Matrix Transposed (GMT) file and parse into a data.frame.

Usage

read_gmt(file)

Arguments

file	Character, a path to a file.

Value

Returns a data.frame with three columns:

• 'ontology_id': Ontology identifier that uniquely identifies the element within the referenced ontology.

• 'ontology_name': Ontology name or description that provides a user-friendly label or textual description for the 'ontology_id'.

• 'list_of_values': Associated genes or proteins that is a vector of identifiers of genes or proteins belonging to the 'ontology_id'.

Examples

# import example gene set
library(mulea)
tf_gmt <- read_gmt(file = system.file(
    package="mulea", "extdata", 
    "Transcription_factor_RegulonDB_Escherichia_coli_GeneSymbol.gmt"))

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