uncouple: Uncouple linked bins

In cancer-genomics/trellis: Somatic structural variant analysis

Uncouple linked bins

Description

Two genomic intervals that are linked are represented by a GRanges object where a single elemnt provides the genomic interval of a bin and a genomic interval of a bin that it is linked to. The latter is included in the metadata (mcols) variable 'linked.to'. This function represents every genomic interval as a single element. Hence, a GRanges of linked intervals with length one would have length-two after uncoupling the bins.

Usage

uncouple(linked_bins)

Arguments

linked_bins

a GRanges representation of two genomic intervals that are linked.

Value

a GRanges object

Examples

linked <- GRanges("chr1", IRanges(1,5))
linked$linked.to <- setNames(GRanges("chr1", IRanges(10, 20)), "b")
names(linked) <- "a"
uncouple(linked)

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.