convert_gmt_file: Create gene lookup

In Benjamin-Vincent-Lab/binfotron: Binfotron Bioinformatics Analysis Tools Suite

Create gene lookup

Description

Uses create_gene_lookup to convert one type of gmt file to another. If using the default value for db_object(org.Hs.eg.db) the values for the inputs and outputs include any listed in https://www.bioconductor.org/help/course-materials/2014/useR2014/Integration.html, although the most common will likely be: ENTREZID, ACCNUM, ALIAS, UNIGENE, ENSEMBL, ENSEMBLPROT, ENSEMBLTRANS, GENENAME, UNIPROT, OMIM, UCSCKG, SYMBOL

Usage

convert_gmt_file(
  input_path,
  input_type,
  output_type,
  output_path,
  db_object = NULL,
  na_string = "NA",
  input_readme_path = NULL
)

Arguments

input_path	Path to the gmt file you would like ot convert.
input_type	Typically ENTREZID or SYMBOL. See decription.
output_type	Typically SYMBOL or ENTREZID. See decription.
output_path	Full path to output gmt file.
db_object	AnnotationDb object. If left null it will be set to org.Hs.eg.db. Passed to create_gene_lookup.
na_string	String to fill in the na positions of a gmt file. Typically "NA" or "".
input_readme_path	Optional path to readme to import into this gmt's readme.

Details

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ convert_gmt_file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Value

None

Benjamin-Vincent-Lab/binfotron documentation built on April 11, 2025, 10:05 p.m.