non_overlaps: Generate non-overlapping intron coordinates

Description Usage Arguments Value Examples

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

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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

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## 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)

asrinivasan-oa/gread documentation built on May 10, 2019, 2:04 p.m.