nBasesMH: Calculate the number of bases that are homologous to the 3'...
In UMCUGenetics/mutSigExtractor: Extracts SNV, indel, DBS, and SV signatures from vcf files.
nBasesMH R Documentation
Calculate the number of bases that are homologous to the 3' flanking sequence
Description
Helper function for extractSigsIndel(). Scans a maximum of 1 indel length from
5' to 3' in the flanking sequence to detect identical bases. Stops prematurely if a
non-identical base is found.
DSBs can be repaired using 3' microhomology, which can be present relative to either the +
or - strand. Therefore, both left and right flanking sequences of the indel need to be
considered. When calculating left flanking homology (i.e. homology in the 3' direction for
the - strand), the reverse complement of the indel sequence and flanking sequence need to
be taken. However, the reverse can be taken for the calculation to save computation.
Usage
nBasesMH(indel.seq, flank.seq, indel.len)
Arguments
indel.seq
The indel sequence as a character
flank.seq
The flanking sequence as a character
Value
An integer stating the number of bases in microhomology
UMCUGenetics/mutSigExtractor documentation built on Aug. 30, 2024, 2:12 p.m.
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| nBasesMH | R Documentation |
Calculate the number of bases that are homologous to the 3' flanking sequence
Description
Helper function for extractSigsIndel(). Scans a maximum of 1 indel length from 5' to 3' in the flanking sequence to detect identical bases. Stops prematurely if a non-identical base is found.
DSBs can be repaired using 3' microhomology, which can be present relative to either the + or - strand. Therefore, both left and right flanking sequences of the indel need to be considered. When calculating left flanking homology (i.e. homology in the 3' direction for the - strand), the reverse complement of the indel sequence and flanking sequence need to be taken. However, the reverse can be taken for the calculation to save computation.
Usage
nBasesMH(indel.seq, flank.seq, indel.len)
Arguments
indel.seq |
The indel sequence as a character |
flank.seq |
The flanking sequence as a character |
Value
An integer stating the number of bases in microhomology
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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