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", ...)

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)
#> # A tibble: 91 x 4
#>    gene_id         seqid start   end
#>    <chr>           <chr> <int> <int>
#>  1 ENSG00000223972 chr1   1737  2090
#>  2 ENSG00000223972 chr1   1873  1920
#>  3 ENSG00000223972 chr1   2042  2090
#>  4 ENSG00000223972 chr1   2476  2560
#>  5 ENSG00000223972 chr1   2476  2584
#>  6 ENSG00000223972 chr1   2838  2915
#>  7 ENSG00000223972 chr1   3084  3237
#>  8 ENSG00000223972 chr1   3084  4275
#>  9 ENSG00000223972 chr1   3316  3533
#> 10 ENSG00000227232 chr1   4226  4692
#> # ... with 81 more rows