indelSeqFlanksStartEnd: Get the start/end positions for the left/right flanks of an...

In UMCUGenetics/mutSigExtractor: Extracts SNV, indel, DBS, and SV signatures from vcf files.

Get the start/end positions for the left/right flanks of an indel

Description

Helper function for extractSigsIndel(), getting flank start/end positions first, then retrieving the sequences using getSeq with a vectorized input improves speed significantly.

Usage

indelSeqFlanksStartEnd(
  chrom,
  pos,
  indel.len,
  indel.type,
  n.indel.lengths.l = 1,
  n.indel.lengths.r = 1
)

Arguments

chrom	A character stating the chromosome
pos	The REF position as an integer
indel.len	The length of the indel as an integer
indel.type	A character stating whether the indel is an insertion ('ins') or deletion ('del')
n.indel.lengths.l	The length of the flanking sequence to return (measured in indel lengths)
n.indel.lengths.r	See n.indel.lengths.l

Value

A vector of the left flank start/end position and right flank start/end position

UMCUGenetics/mutSigExtractor documentation built on Aug. 30, 2024, 2:12 p.m.