filterForSignature: Filter a with tri-nucleotide context annotated list of loci...

In Wedge-lab/dpclust3p: Dirichlet Process Clustering Pre-Processing Package

Filter a with tri-nucleotide context annotated list of loci for a particular signature supplied as a regex like so: (CAG)|(CTG)|(GAC)|(GTC).

Description

Filter a with tri-nucleotide context annotated list of loci for a particular signature supplied as a regex like so: (CAG)|(CTG)|(GAC)|(GTC).

Usage

filterForSignature(
  signature_anno_loci_file,
  signature_regex,
  outfile,
  trinucleotide_column = 5,
  alt_alleles = NA,
  alt_allele_column = 4
)

Arguments

signature_anno_loci_file	Filepath to a with tri-nucleotide context annotated loci
signature_regex	A regex that captures the signature to keep.
outfile	Filepath to where to store the output.
trinucleotide_column	Integer representing the column within the input file that contains the context
alt_alleles	An optional vector with reference alleles to allow.
alt_allele_column	The column in the annotated loci file that contains the reference base.

Author(s)

sd11

Wedge-lab/dpclust3p documentation built on June 14, 2025, 4:24 p.m.