collect_parts: Collect and combine intronic/exonic parts by gene

In sa-lee/superintronic: Tools for Working with Intron Signal

Description

Collect and combine intronic/exonic parts by gene

Usage

collect_parts(annotation, ...)

## S4 method for signature 'GRanges'
collect_parts(annotation, ...)

## S4 method for signature 'character'
collect_parts(annotation, ...)

## S4 method for signature 'GFFFile'
collect_parts(annotation, ...)

## S4 method for signature 'TxDb'
collect_parts(annotation)

Arguments

annotation	an object representing an annotation such as an GenomicFeatures::TxDb, a GenomicRanges::GRanges object obtained from rtracklayer::import() or plyranges::read_gff() or the name of GFF/GTF file.
...	optional arguments to be passed to downstream methods

Details

This function takes an annotation object and returns a GRanges object with number of rows equal to the number of gene features contained. The resulting GRanges object has the following additional metadata columns:

• exonic_parts: a GRangesList column containing the exonic regions for each gene, obtained from type == 'exon' in GFF/GTF file. In the case of a TxDb object, this is obtained by GenomicFeatures::exonBy.

• intronic_parts: a GRangesList column containing the intronic regions for each gene. This is simply defined as the parallel set difference betweeen the gene ranges and the exonic ranges.

• n_olaps: the integer count of the number times a gene overlaps any other gene in the annotation.

Value

a GRanges object

Examples

gtf <- system.file("extdata", "Homo_sapiens.GRCh37.75_subset.gtf", package = "airway")
collect_parts(gtf)

sa-lee/superintronic documentation built on Feb. 18, 2020, 10:36 a.m.