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

cast_gtf_to_genes

R Documentation

Function to extract exon names and positions from a gtf file

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

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

`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

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

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