nCopiesAlongFlank: Calculate the number of copies of the indel sequence are...
In UMCUGenetics/mutSigExtractor: Extracts SNV, indel, DBS, and SV signatures from vcf files.
nCopiesAlongFlank R Documentation
Calculate the number of copies of the indel sequence are present in the flank sequence
Description
Helper function for extractSigsIndel(). Scans along the flanking sequence for
copies of the indel sequence using a sliding window with a length equal to the length of
the indel sequence. The sliding window jumps in increments equal to the indel length.
Scanning stops prematurely when the indel sequence does not match the one in the sliding
window. The indel sequence itself counts as one copy.
Scanning needs only to be done from the 5' -> 3' direction as the reported POS of an indel
in a repeat region is always the first position of the repeat region.
Usage
nCopiesAlongFlank(indel.seq, flank.seq)
Arguments
indel.seq
The indel sequence as a character
flank.seq
The flanking sequence as a character
Value
An integer stating the number of copies found in the flanking sequence
UMCUGenetics/mutSigExtractor documentation built on Aug. 30, 2024, 2:12 p.m.
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| nCopiesAlongFlank | R Documentation |
Calculate the number of copies of the indel sequence are present in the flank sequence
Description
Helper function for extractSigsIndel(). Scans along the flanking sequence for copies of the indel sequence using a sliding window with a length equal to the length of the indel sequence. The sliding window jumps in increments equal to the indel length. Scanning stops prematurely when the indel sequence does not match the one in the sliding window. The indel sequence itself counts as one copy.
Scanning needs only to be done from the 5' -> 3' direction as the reported POS of an indel in a repeat region is always the first position of the repeat region.
Usage
nCopiesAlongFlank(indel.seq, flank.seq)
Arguments
indel.seq |
The indel sequence as a character |
flank.seq |
The flanking sequence as a character |
Value
An integer stating the number of copies found in the flanking sequence
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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