API for rcastelo/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
rcastelo/VariantFiltering documentation built on Feb. 11, 2021, 11:38 p.m.