Get1BPIndelFlanks: 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

Description

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

Usage

Get1BPIndelFlanks(sequence, ref, alt, indel.class, flank.length = 5)

Arguments

sequence	A string from seq.context column from in-memory data.frame or similar table containing "VCF" (variant call format) data as created by AnnotateIDVCF.
ref	A string from REF column from in-memory data.frame or similar table containing "VCF" (variant call format) data as created by AnnotateIDVCF.
alt	A string from ALT column from in-memory data.frame or similar table containing "VCF" (variant call format) data as created by AnnotateIDVCF.
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 / 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 string for the specified sequence and indel.class.

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