rearrangedReads: Identify rearranged reads - initiallly unmapped reads that...

In cancer-genomics/trellis: Somatic structural variant analysis

Identify rearranged reads – initiallly unmapped reads that can be aligned by blat to span a novel sequence junction.

Description

Identify rearranged reads – initiallly unmapped reads that can be aligned by blat to span a novel sequence junction.

Usage

rearrangedReads(linked_bins, blat, maxgap = 500)

Arguments

linked_bins	a GRanges of linked bins (e.g., gotten by linkedBins(rearrangement.list))
blat	a data.frame of blat alignment records
maxgap	this maximum gap between the mapped read and the genomic intervals of the improper read clusters

Value

a 'GRangesList' of blat records that map to both sides of a sequence junction. Each list element corresponds to one read that is aligned to two locations (i.e., each element of the list consists of the vector of reads that supports one rearrangement).

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