collapse_gr {seqsetvis} | R Documentation |
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.
collapse_gr(genome_gr)
genome_gr |
a GRanges of regions on a single chromosome. Regions are intended to be non-contiguous and may even overlap. |
a new GRanges object with same mcols as input with all intervals starting at 1 and no empty space between syntenic regions.
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)