Given a deletion and its sequence context, categorize it
This function is primarily for internal use, but we export it to document the underlying logic.
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 |
The deleted sequence in |
pos |
The position of |
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.)
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"Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.