%na% |
Replaces the NA values in a with corresponding values in b |
%null% |
Uses b if a is NULL |
.breakpointRanges |
Extracting the structural variants as a GRanges. |
.constrict |
constrict |
.isSymbolic |
Determining whether the variant is a symbolic allele. |
.pairwiseLCPrefix |
vectorised pairwise longest common prefix Returns the length of the longest common prefix for each string pair |
.svLen |
Returns the structural variant length of the first allele |
.testfile |
Testthat helper utility to locate files used for package tests |
.testrecord |
Loading a VCF containing the given records |
.toVcfBreakendNotationAlt |
Converts to breakend notation |
.unXStringSet |
converts an XStringSet to a character |
align_breakpoints |
Adjusting the nominal position of a pair of partnered breakpoint. |
breakendRanges |
Extracting unpartnered breakend structural variants as a GRanges |
breakendRanges-method |
Extracting unpartnered breakend structural variants as a GRanges |
breakpointgr2bedpe |
Converting breakpoint GRanges to BEDPE-like dataframe |
breakpointgr2pairs |
Converts a breakpoint GRanges object to a Pairs object |
breakpointGRangesToVCF |
Converts the given breakpoint GRanges object to VCF format in breakend notation. |
breakpointRanges |
Extracting the structural variants as a GRanges. |
breakpointRanges-method |
Extracting the structural variants as a GRanges. |
calculateReferenceHomology |
Calculates the length of inexact homology between the breakpoint sequence and the reference |
countBreakpointOverlaps |
Counting overlapping breakpoints between two breakpoint sets |
elementExtract |
Extracts the element of each element at the given position |
extractBreakpointSequence |
Extracts the breakpoint sequence. |
extractReferenceSequence |
Returns the reference sequence around the breakpoint position |
findBreakpointOverlaps |
Finding overlapping breakpoints between two breakpoint sets |
findInsDupOverlaps |
Finds duplication events that are reported as inserts. As sequence alignment algorithms do no allow backtracking, long read-based variant callers will frequently report small duplication as insertion events. Whilst both the duplication and insertion representations result in the same sequence, this representational difference is problematic when comparing variant call sets. |
isStructural |
Determining whether the variant is a structural variant |
isStructural-method |
Determining whether the variant is a structural variant |
isSymbolic |
Determining whether the variant is a symbolic allele. |
isSymbolic-method |
Determining whether the variant is a symbolic allele. |
pairs2breakpointgr |
Converts a breakpoint GRanges object to a Pairs object |
partner |
GRanges representing the breakend coordinates of structural variants #@export Partner breakend for each breakend. |
simpleEventLength |
Length of event if interpreted as an isolated breakpoint. |
simpleEventType |
Type of simplest explaination of event. Possible types are: | Type | Description | | BND | Single breakend | | CTX | Interchromosomal translocation | | INV | Inversion. Note that both ++ and - breakpoint will be classified as inversion regardless of whether the matching breakpoint actually exists | | DUP | Tandem duplication | | INS | Insertion | | DEL | Deletion | |
StructuralVariantAnnotation |
StructuralVariantAnnotation: a package for SV annotation |