non_overlaps: Generate non-overlapping intron coordinates

In openanalytics/gread: Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files

Description

This function takes an gtf/gff object. If the features exon and intron are present, then, it attempts to find a set of exon and intron coordinates that do NOT overlap with each other. If the intron coordinates are not present, it constructs the introns first using gread::construct_introns and then attempts to extract non-overlapping exonic and intronic coordinates. If exon feature is not present, it returns an error.

Note: This function is not exported at the moment.

Usage

non_overlaps(x, transcript_id = "transcript_id", gene_id = "gene_id")

Arguments

x	An object of class gtf/gff object which has to have features intron and exon.
transcript_id	Column name in x corresponding to transcript id.
gene_id	Column name in x corresponding to gene id.

Value

Returns a list of GRanges objects containing non overlapping exons and non overlapping introns.

Examples

## Not run: 
path <- system.file("tests", package="gread")
gtf_file <- file.path(path, "sample.gtf")
gtf <- read_format(gtf_file)
non_overlaps(gtf)

## End(Not run)

openanalytics/gread documentation built on May 24, 2019, 2:29 p.m.