API for VariantFiltering
Filtering of coding and non-coding genetic variants

Global functions
$,VariantFilteringParam-method	Man page
.aMat2edgeList	Source code
.adjustForStrandSense	Source code
.ancestorsSO	Source code
.autosomalDominantFilter	Source code
.autosomalDominantMask	Source code
.autosomalRecessiveHomozygousFilter	Source code
.autosomalRecessiveHomozygousMask	Source code
.availablePackages	Source code
.bsgenomepkgs	Source code
.buildAncestorsMatrix	Source code
.buildDescendantsMatrix	Source code
.cDNAloc	Source code
.checkValueCutoffArgs	Source code
.deNovoFilter	Source code
.deNovoMask	Source code
.descendantsSO	Source code
.emptyAnnotations	Source code
.findSOIDs	Source code
.fiveSpliceSites	Source code
.getOS	Source code
.io_check_exists	Source code
.io_exists_mask	Source code
.isPkgLoaded	Source code
.loadAnnotationPackageObject	Source code
.loadPrecomputedVariantFilteringResults	Source code
.loc2SNPid	Source code
.loc2XtraSNPid	Source code
.loc2dbSNPid	Source code
.locateAllVariants	Source code
.location	Source code
.matchSeqinfo	Source code
.normalizePath	Source code
.onLoad	Source code
.orgdbpkgs	Source code
.otherannotations	Source code
.ppath	Source code
.readPEDfile	Source code
.scoreBindingSiteVariants	Source code
.scoreBindingSiteVariantsThisWM	Source code
.snpdbpkgs	Source code
.threeSpliceSites	Source code
.txdbpkgs	Source code
.xLinkedFilter	Source code
.xLinkedMask	Source code
.xtrasnpdbpkgs	Source code
CutoffsList	Man page Source code
CutoffsList-class	Man page
FiveSpliceSiteVariants	Man page Source code
FiveSpliceSiteVariants-class	Man page
GenePhylostrataDb	Man page Man page Source code
GenePhylostrataDb-class	Man page
MAFpop	Man page
MAFpop,VariantFilteringResults-method	Man page
MAFpop<-	Man page
MAFpop<-,VariantFilteringResults,ANY,logical-method	Man page
MAFpop<-,VariantFilteringResults,logical-method	Man page
MAFpop<-,VariantFilteringResults-method	Man page
OMIMpresent	Man page
OMIMpresent,VariantFilteringResults-method	Man page
OMIMpresent<-	Man page
OMIMpresent<-,VariantFilteringResults,character-method	Man page
OMIMpresent<-,VariantFilteringResults-method	Man page
ThreeSpliceSiteVariants	Man page Source code
ThreeSpliceSiteVariants-class	Man page
VariantFiltering	Man page
VariantFiltering-defunct	Man page
VariantFiltering-deprecated	Man page
VariantFiltering-package	Man page
VariantFilteringParam	Man page Source code
VariantFilteringParam-class	Man page
VariantFilteringResults	Man page
VariantFilteringResults-class	Man page
WeightMatrix	Man page
WeightMatrix-class	Man page
aaChangeType	Man page
aaChangeType,VariantFilteringResults-method	Man page
aaChangeType<-	Man page
aaChangeType<-,VariantFilteringResults,character-method	Man page
addSOmetadata	Source code
allVariants	Man page
allVariants,VariantFilteringResults-method	Man page
aminoAcidChanges	Source code
annoGroups	Man page
annoGroups,VariantFilteringResults-method	Man page
annotateSO	Source code
annotationEngine	Source code
autosomalDominant	Man page
autosomalDominant,VariantFilteringParam-method	Man page
autosomalRecessiveHeterozygous	Man page
autosomalRecessiveHeterozygous,VariantFilteringParam-method	Man page
autosomalRecessiveHomozygous	Man page
autosomalRecessiveHomozygous,VariantFilteringParam-method	Man page
bamFiles	Man page
bamFiles,VariantFilteringResults-method	Man page
bamFiles<-	Man page
bamFiles<-,VariantFilteringResults,BamViews-method	Man page
bamFiles<-,VariantFilteringResults-method	Man page
browseVariants	Man page Source code
change	Man page
change<-	Man page
change<-,CutoffsList	Man page
change<-,CutoffsList,ANY,character-method	Man page
change<-,CutoffsList,ANY,integer-method	Man page
change<-,CutoffsList,ANY,logical-method	Man page
change<-,CutoffsList,ANY,numeric-method	Man page
class:CutoffsList	Man page
class:VariantFilteringParam	Man page
class:VariantFilteringResults	Man page
conservedPositions	Man page
conservedPositions,WeightMatrix-method	Man page
cutoffs	Man page
cutoffs,VariantFilteringParam-method	Man page
cutoffs,VariantFilteringResults-method	Man page
cutoffs<-	Man page
cutoffs<-,VariantFilteringResults,CutoffsList-method	Man page
cutoffs<-,VariantFilteringResults,logical-method	Man page
cutoffs<-,VariantFilteringResults-method	Man page
dbSNPpresent	Man page
dbSNPpresent,VariantFilteringResults-method	Man page
dbSNPpresent<-	Man page
dbSNPpresent<-,VariantFilteringResults,ANY-method	Man page
dbSNPpresent<-,VariantFilteringResults-method	Man page
deNovo	Man page
deNovo,VariantFilteringParam-method	Man page
downstream	Man page
downstream,FiveSpliceSiteVariants-method	Man page
downstream,ThreeSpliceSiteVariants-method	Man page
downstream<-	Man page
downstream<-,FiveSpliceSiteVariants-method	Man page
downstream<-,ThreeSpliceSiteVariants-method	Man page
fetchKnownVariantsByID	Man page
fetchKnownVariantsByID,MafDb-method	Man page
filteredVariants	Man page
filteredVariants,VariantFilteringResults-method	Man page
filters	Man page
filters,VariantFilteringParam-method	Man page
filters,VariantFilteringResults-method	Man page
filters<-	Man page
filters<-,VariantFilteringResults-method	Man page
filtersMetadata	Man page
filtersMetadata,VariantFilteringParam-method	Man page
filtersMetadata,VariantFilteringResults-method	Man page
genePhylostrata	Man page
genePhylostrata,GenePhylostrataDb-method	Man page
genePhylostratum	Man page
genePhylostratum,GenePhylostrataDb,character-method	Man page
genePhylostratum,GenePhylostrataDb,missing-method	Man page
genePhylostratum,GenePhylostrataDb-method	Man page
humanGenesPhylostrata	Man page
inheritanceModel	Man page
inheritanceModel,VariantFilteringResults-method	Man page
length	Man page
length,VariantFilteringResults-method	Man page
maxMAF	Man page
maxMAF,VariantFilteringResults-method	Man page
maxMAF<-	Man page
maxMAF<-,VariantFilteringResults,numeric-method	Man page
minCUFC	Man page
minCUFC,VariantFilteringResults-method	Man page
minCUFC<-	Man page
minCUFC<-,VariantFilteringResults,numeric-method	Man page
minIntronLength	Man page
minIntronLength,FiveSpliceSiteVariants-method	Man page
minIntronLength,ThreeSpliceSiteVariants-method	Man page
minIntronLength<-	Man page
minIntronLength<-,FiveSpliceSiteVariants-method	Man page
minIntronLength<-,ThreeSpliceSiteVariants-method	Man page
minPhastCons	Man page
minPhastCons,VariantFilteringResults-method	Man page
minPhastCons<-	Man page
minPhastCons<-,VariantFilteringResults,ANY-method	Man page
minPhastCons<-,VariantFilteringResults-method	Man page
minPhylostratum	Man page
minPhylostratum,VariantFilteringResults-method	Man page
minPhylostratum<-	Man page
minPhylostratum<-,VariantFilteringResults,ANY-method	Man page
minPhylostratum<-,VariantFilteringResults-method	Man page
minScore3ss	Man page
minScore3ss,VariantFilteringResults-method	Man page
minScore3ss<-	Man page
minScore3ss<-,VariantFilteringResults,ANY-method	Man page
minScore3ss<-,VariantFilteringResults-method	Man page
minScore5ss	Man page
minScore5ss,VariantFilteringResults-method	Man page
minScore5ss<-	Man page
minScore5ss<-,VariantFilteringResults,ANY-method	Man page
minScore5ss<-,VariantFilteringResults-method	Man page
naMAF	Man page
naMAF,VariantFilteringResults-method	Man page
naMAF<-	Man page
naMAF<-,VariantFilteringResults,logical-method	Man page
names,VariantFilteringParam-method	Man page
organism,GenePhylostrataDb-method	Man page
param	Man page
param,VariantFilteringResults-method	Man page
plot,VariantFilteringResults,ANY-method	Man page
readAAradicalChangeMatrix	Man page Source code
readWm	Man page Source code
referenceGenome,VariantFilteringResults-method	Man page
reportVariants	Man page
reportVariants,VariantFilteringResults-method	Man page
resetSamples	Man page
resetSamples,VariantFilteringResults-method	Man page
samples	Man page
samples,VariantFilteringResults-method	Man page
samples<-	Man page
samples<-,VariantFilteringResults,character-method	Man page
samples<-,VariantFilteringResults-method	Man page
sequence_variant.gSOXP	Man page
show,CompressedVRangesList-method	Man page
show,FiveSpliceSiteVariants-method	Man page
show,GenePhylostrataDb-method	Man page
show,ThreeSpliceSiteVariants-method	Man page
show,VariantFilteringParam-method	Man page
show,VariantFilteringResults-method	Man page
show,VariantFilteringResultsUI-method	Man page
show,WeightMatrix-method	Man page
softFilterMatrix,VariantFilteringResults-method	Man page
softFilterMatrix<-,VariantFilteringResults-method	Man page
sog	Man page
sog,VariantFilteringParam-method	Man page
sog,VariantFilteringResults-method	Man page
sortings	Man page
sortings,VariantFilteringResults-method	Man page
sortings<-	Man page
sortings<-,VariantFilteringResults,CutoffsList-method	Man page
spliceSiteMatricesHuman	Man page Source code
summary,VariantFilteringResults-method	Man page
tabPanelAbout	Source code
typeOfVariants	Source code
unrelatedIndividuals	Man page
unrelatedIndividuals,VariantFilteringParam-method	Man page
upstream	Man page
upstream,FiveSpliceSiteVariants-method	Man page
upstream,ThreeSpliceSiteVariants-method	Man page
upstream<-	Man page
upstream<-,FiveSpliceSiteVariants-method	Man page
upstream<-,ThreeSpliceSiteVariants-method	Man page
variantConsequence	Man page
variantConsequence,VariantFilteringResults-method	Man page
variantConsequence<-	Man page
variantConsequence<-,VariantFilteringResults,ANY,logical-method	Man page
variantConsequence<-,VariantFilteringResults,logical-method	Man page
variantConsequence<-,VariantFilteringResults-method	Man page
variantHGVS	Source code
variantLocation	Man page
variantLocation,VariantFilteringResults-method	Man page
variantLocation<-	Man page
variantLocation<-,VariantFilteringResults,ANY,logical-method	Man page
variantLocation<-,VariantFilteringResults,logical-method	Man page
variantLocation<-,VariantFilteringResults-method	Man page
variantLocations	Man page Source code
variantType	Man page
variantType,VariantFilteringResults-method	Man page
variantType<-	Man page
variantType<-,VariantFilteringResults,ANY,logical-method	Man page
variantType<-,VariantFilteringResults,logical-method	Man page
variantType<-,VariantFilteringResults-method	Man page
width,WeightMatrix-method	Man page
wmFilename	Man page
wmFilename,WeightMatrix-method	Man page
wmLocations	Man page
wmLocations,WeightMatrix-method	Man page
wmLocations<-	Man page
wmLocations<-,WeightMatrix,character-method	Man page
wmLocations<-,WeightMatrix-method	Man page
wmName	Man page
wmName,WeightMatrix-method	Man page
wmScore	Man page
wmScore,WeightMatrix,DNAStringSet-method	Man page
wmScore,WeightMatrix,character-method	Man page
wmScore,character,DNAStringSet-method	Man page
wmScore,character,character-method	Man page
wmStrictLocations	Man page
wmStrictLocations,WeightMatrix-method	Man page
wmStrictLocations<-	Man page
wmStrictLocations<-,WeightMatrix,logical-method	Man page
wmStrictLocations<-,WeightMatrix-method	Man page
xLinked	Man page
xLinked,VariantFilteringParam-method	Man page