cast_gtf_to_genes: Function to extract exon names and positions from a gtf file

In noisyr: Noise Quantification in High Throughput Sequencing Output

Description

This function is used to extract all exons and their positions in the genome from an input gtf file.

Usage

cast_gtf_to_genes(filename, feature = "exon", att_of_interest = "gene_id", ...)

Arguments

filename	path to the gtf file
feature	the feature type name to filter the feature (3rd) column of the gtf/gff file; default is exon
att_of_interest	the attribute to extract from the last column of the gtf/gff file; default in gene_id
...	arguments passed on to other methods

Value

A tibble of the ids, gene names, chromosomes, start and end positions of each exon found in the gtf file.

Examples

fl <- system.file("extdata", "example.gtf.gz", package="Rsamtools", mustWork=TRUE)
cast_gtf_to_genes(fl)

noisyr documentation built on April 16, 2021, 5:07 p.m.