parse_GTF_info: Process GTF file.

In laurabiggins/GOcategoryStats: Provides statistics for Gene Ontology categories (Title Case)

Description

parses the info column of a GTF file to extract the gene name and length.

Usage

parse_GTF_info(gtf, gene_names = TRUE, gene_length = TRUE,
  remove_duplicates = TRUE)

Arguments

gtf	gtf file that has been imported using import_GTF. The gtf file must include a column named info that contains data in the following format: a character vector in the format "gene_id "ENSMUSG00000102693"; gene_version "1"; gene_name "4933401J01Rik"; gene_source "havana"; gene_biotype "TEC"
gene_names	if true, add a column containing gene name
gene_length	if true, add a column containing gene length
remove_duplicates	remove rows if gene names are duplicated. The row that is kept is the first instance of that gene. To remove duplicates based on something other that gene name, use the separate remove_duplicates function.

Value

A data frame containing all the genes from gtf_file

Examples

parse_GTF_info(gtf_file)

laurabiggins/GOcategoryStats documentation built on Oct. 27, 2019, 11:36 a.m.