SymmetricalContextsFor1BPIndel: Get all the sequence contexts of the indels in a given 1...

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Get all the sequence contexts of the indels in a given 1 base-pair indel class from a VCF

Description

Get all the sequence contexts of the indels in a given 1 base-pair indel class from a VCF

Usage

SymmetricalContextsFor1BPIndel(annotated.vcf, indel.class, flank.length = 5)

Arguments

annotated.vcf	An in-memory data.frame or similar table containing "VCF" (variant call format) data as created by VCFsToIDCatalogs with argument return.annotated.vcfs = TRUE.
indel.class	A single character string that denotes a 1 base pair insertion or deletion, as taken from ICAMS::catalog.row.order$ID. Insertions or deletions into or from 5+ base-pair homopolymers are not supported.
flank.length	The length of flanking bases around the position or homopolymer targeted by the indel.

Value

A list of all sequence contexts for the specified indel.class.

ICAMS documentation built on June 15, 2025, 1:08 a.m.