Man pages for lachlanmcintosh/SAP
A SNP analysis pipeline

aggregateFunctionsForReturns a list of aggegration functions for the given variant...
blastHomologyIdentifies breakpoint sequences with signficant homology to...
breakpointRangesExtracts the structural variants as a BreakendGRanges
breakpointSequenceExtracts the breakpoint sequence.
elementExtractExtracts the element of each element at the given position
findBreakpointOverlapsFinds overlapping breakpoints by requiring that breakends on...
grapes-na-grapesReplaces the NA values in a with corresponding values in b
grapes-null-grapesUses b if a is NULL
isStructuralDetermines whether the variant is a structural variant
isSymbolicDetermines whether the variant is a symbolic allele
partnerGRanges representing the breakend coordinates of structural...
referenceHomologyCalculates the length of inexact homology between the...
referenceSequenceReturns the reference sequence around the breakpoint position
transformFunctionsForReturns a list of transformation functions for the given...
unpackExpands any columns with multiple values (such as Lists) into...
lachlanmcintosh/SAP documentation built on May 21, 2017, 8:27 a.m.