calculateReferenceHomology {StructuralVariantAnnotation} | R Documentation |
Calculates the length of inexact homology between the breakpoint sequence and the reference
calculateReferenceHomology(gr, ref, anchorLength = 300, margin = 5, match = 2, mismatch = -6, gapOpening = 5, gapExtension = 3)
gr |
reakpoint 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 |
see Biostrings::pairwiseAlignment |
mismatch |
see Biostrings::pairwiseAlignment |
gapOpening |
see Biostrings::pairwiseAlignment |
gapExtension |
see Biostrings::pairwiseAlignment |
A dataframe containing the length of inexact homology between the breakpoint sequence and the reference.