Canonicalize1Del: Given a deletion and its sequence context, categorize it
In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Description Usage Arguments Details Value Examples

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

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

`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.

See https://github.com/steverozen/ICAMS/raw/master/data-raw/PCAWG7_indel_classification_2017_12_08.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.

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.)

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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"