referenceHomology: Calculates the length of inexact homology between the...
In lachlanmcintosh/SAP: A SNP analysis pipeline
Description
Calculates the length of inexact homology between the breakpoint sequence
and the reference
Usage
1
2
referenceHomology(gr, ref, anchorLength = 300, margin = 5, match = 2,
mismatch = -6, gapOpening = 5, gapExtension = 3)
Arguments
gr
breakpoint GRanges
ref
Reference BSgenome
anchorLength
Number of bases to consider for homology
margin
Number of additional reference bases include. This allows
for inexact homology to be detected even in the presence of indels.
match
alignment
mismatch
see Biostrings::pairwiseAlignment
gapOpening
see Biostrings::pairwiseAlignment
gapExtension
see Biostrings::pairwiseAlignment
match
see Biostrings::pairwiseAlignment
lachlanmcintosh/SAP documentation built on May 20, 2019, 7:32 p.m.
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Description
Calculates the length of inexact homology between the breakpoint sequence and the reference
Usage
1 2 | referenceHomology(gr, ref, anchorLength = 300, margin = 5, match = 2,
mismatch = -6, gapOpening = 5, gapExtension = 3)
|
Arguments
gr |
breakpoint GRanges |
ref |
Reference BSgenome |
anchorLength |
Number of bases to consider for homology |
margin |
Number of additional reference bases include. This allows for inexact homology to be detected even in the presence of indels. |
match |
alignment |
mismatch |
see Biostrings::pairwiseAlignment |
gapOpening |
see Biostrings::pairwiseAlignment |
gapExtension |
see Biostrings::pairwiseAlignment |
match |
see Biostrings::pairwiseAlignment |
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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