collapse_gr: collapse_gr

In seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

Description

collapse non-contiguous regions (i.e. exons) into a contiguous coordinate starting at 1. this is strand sensitive and intended for use with all exons of a single gene.

Usage

collapse_gr(genome_gr)

Arguments

genome_gr

a GRanges of regions on a single chromosome. Regions are intended to be non-contiguous and may even overlap.

Value

a new GRanges object with same mcols as input with all intervals starting at 1 and no empty space between syntenic regions.

Examples

library(data.table)
library(GenomicRanges)
dev_dat = data.table(seqnames = "chrTest",
                     transcript_id = c(1, 1,  2, 2, 3, 3, 3),
                     start = c(5,  30,  8, 30, 2, 30, 40),
                     end = c(10, 35, 15, 38, 7, 35, 45),
                     strand = "+")

genome_gr = GRanges(dev_dat)
collapse_gr(genome_gr)

neg_gr = genome_gr
strand(neg_gr) = "-"
collapse_gr(neg_gr)

seqsetvis documentation built on Nov. 8, 2020, 5:57 p.m.