Canonicalize1Del {ICAMS}

Given a deletion and its sequence context, categorize it

Description

This function is primarily for internal use, but we export it to document the underlying logic.

Usage

Canonicalize1Del(context, del.seq, pos, trace = 0)

Arguments

context

The deleted sequence plus ample surrounding sequence on each side (at least as long as del.seq).

del.seq

The deleted sequence in context.

pos

The position of del.sequence in context.

trace

If > 0, then generate messages tracing how the computation is carried out.

Details

See https://github.com/steverozen/ICAMS/blob/master/data-raw/PCAWG7_indel_classification_2021_09_03.xlsx for additional information on deletion mutation classification.

This function first handles deletions in homopolymers, then handles deletions in simple repeats with longer repeat units, (e.g. CACACACA, see FindMaxRepeatDel), and if the deletion is not in a simple repeat, looks for microhomology (see FindDelMH).

See the code for unexported function CanonicalizeID and the functions it calls for handling of insertions.

Value

A string that is the canonical representation of the given deletion type. 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.)

Examples

Canonicalize1Del("xyAAAqr", del.seq = "A", pos = 3) # "DEL:T:1:2"
Canonicalize1Del("xyAAAqr", del.seq = "A", pos = 4) # "DEL:T:1:2"
Canonicalize1Del("xyAqr", del.seq = "A", pos = 3)   # "DEL:T:1:0"