grab_contig_breakends: grab_contig_breakends

In mskilab/loosends: Classifying loose ends in gGraphs

grab_contig_breakends

Description

Get seed side and mate side breakends for a single contig.

Assumes that a unique qname is supplied. Also assumes that the alignment is split.

If more than one contig is supplied, throws an exception.

Usage

grab_contig_breakends(
  calns,
  seed,
  reduce.pad = 20,
  seed.pad = 1000,
  verbose = FALSE
)

Arguments

calns	(GRanges) contig alignment
seed	(GRanges) seed region of the contig
reduce.pad	(numeric) reduce multipmapping regions using this pad (default 20)
seed.pad	(numeric) bp pad to be considered lying outside peak (default 1e3)
verbose	(logical)

Value

data.table with seqnames, start, end, strand, and a few metadata columns:

• proximal (logical) proximal vs. distal breakends?

• proximal.first (logical) proximal part of the contig is in the first part of the contig

• seed.only (logical) contig is seed only

• mate.only (logical) conig is mate only

• c_type (character)

• c_spec (character)

• cigar (character)

• mapq (numeric) strand is in breakend orientation (so if there were a junction it would be consistent with the junction)

mskilab/loosends documentation built on Aug. 24, 2023, 8:08 a.m.