Canonicalize1ID: Given a single insertion or deletion in context categorize...

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

Given a single insertion or deletion in context categorize it.

Description

Given a single insertion or deletion in context categorize it.

Usage

Canonicalize1ID(context, ref, alt, pos, trace = 0)

Arguments

context	Ample surrounding sequence on each side of the insertion or deletion.
ref	The reference allele (vector of length 1)
alt	The alternative allele (vector of length 1)
pos	The position of ins.or.del.seq in context.
trace	If > 0, then generate messages tracing how the computation is carried out.

Value

A string that is the canonical representation of the type of the given insertion or deletion. Return NA and raise a warning if there is an un-normalized representation of the deletion of a repeat unit. See FindDelMH for details. (This seems to be very rare.)

ICAMS documentation built on June 22, 2024, 6:47 p.m.