Man pages for lachlanmcintosh/SAP
A SNP analysis pipeline
| aggregateFunctionsFor | Returns a list of aggegration functions for the given variant... |
| blastHomology | Identifies breakpoint sequences with signficant homology to... |
| breakpointRanges | Extracts the structural variants as a BreakendGRanges |
| breakpointSequence | Extracts the breakpoint sequence. |
| elementExtract | Extracts the element of each element at the given position |
| findBreakpointOverlaps | Finds overlapping breakpoints by requiring that breakends on... |
| grapes-na-grapes | Replaces the NA values in a with corresponding values in b |
| grapes-null-grapes | Uses b if a is NULL |
| isStructural | Determines whether the variant is a structural variant |
| isSymbolic | Determines whether the variant is a symbolic allele |
| partner | GRanges representing the breakend coordinates of structural... |
| referenceHomology | Calculates the length of inexact homology between the... |
| referenceSequence | Returns the reference sequence around the breakpoint position |
| transformFunctionsFor | Returns a list of transformation functions for the given... |
| unpack | Expands any columns with multiple values (such as Lists) into... |
