harmonize_seqlengths: harmonize_seqlengths

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

Description

ensures compatibility between seqlength of gr and bam_file based on header

Usage

harmonize_seqlengths(gr, bam_file)

Arguments

gr	GRanges, object to harmonize seqlengths for
bam_file	character, a path to a valid bam file

Value

gr with seqlengths matching bam_file

Examples

library(GenomicRanges)
gr = GRanges("chr1", IRanges(1, 100))
#seqlengths has not been set
seqlengths(gr)
bam = system.file("extdata/test.bam", package = "seqsetvis")
gr2 = harmonize_seqlengths(gr, bam)
#seqlengths now set
seqlengths(gr2)

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