API for Bioconductor-mirror/VariantFiltering
Filtering of coding and non-coding genetic variants

Global functions
$,MafDb-method Man page
$,MafDb2-method Man page
$,VariantFilteringParam-method 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
MafDb Man page Source code
MafDb-class Man page
MafDb2 Man page Source code
MafDb2-class 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
aMat2edgeList Source code
aaChangeType Man page
aaChangeType,VariantFilteringResults-method Man page
aaChangeType<- Man page
aaChangeType<-,VariantFilteringResults,character-method Man page
adjustForStrandSense Source code
allVariants Man page
allVariants,VariantFilteringResults-method Man page
aminoAcidChanges Source code
ancestorsSO Source code
annoGroups Man page
annoGroups,VariantFilteringResults-method Man page
annotateSO Source code
annotateVariants Man page
annotateVariants,GScores-method Man page
annotateVariants,GenePhylostrataDb-method Man page
annotateVariants,MafDb-method Man page
annotateVariants,MafDb2-method Man page
annotateVariants,OrgDb-method Man page
annotateVariants,PROVEANDb-method Man page
annotateVariants,PolyPhenDb-method Man page
annotateVariants,SNPlocs-method Man page
annotateVariants,TxDb-method Man page
annotateVariants,XtraSNPlocs-method Man page
annotationEngine Source code
autosomalDominant Man page
autosomalDominant,VariantFilteringParam-method Man page
autosomalDominantFilter Source code
autosomalDominantMask Source code
autosomalRecessiveHeterozygous Man page
autosomalRecessiveHeterozygous,VariantFilteringParam-method Man page
autosomalRecessiveHomozygous Man page
autosomalRecessiveHomozygous,VariantFilteringParam-method Man page
autosomalRecessiveHomozygousFilter Source code
autosomalRecessiveHomozygousMask Source code
bamFiles Man page
bamFiles,VariantFilteringResults-method Man page
bamFiles<- Man page
bamFiles<-,VariantFilteringResults,BamViews-method Man page
bamFiles<-,VariantFilteringResults-method Man page
buildAncestorsMatrix Source code
buildDescendantsMatrix Source code
cDNAloc Source code
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-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
deNovoFilter Source code
deNovoMask Source code
decodeRAW2AF2 Source code
descendantsSO Source code
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
emptyAnnotations Source code
extractRawFromRleList Source code Source code
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
findSOIDs Source code
fiveSpliceSites Source code
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
getOS Source code
humanGenesPhylostrata Man page
inheritanceModel Man page
inheritanceModel,VariantFilteringResults-method Man page
length Man page
length,VariantFilteringResults-method Man page
loadAnnotationPackageObject Source code
loadPrecomputedVariantFilteringResults Source code
loc2SNPid Source code
loc2XtraSNPid Source code
loc2dbSNPid Source code
locateAllVariants Source code
location Source code
mafById Man page Man page
mafById,MafDb-method Man page
mafById,MafDb2-method Man page
mafByOverlaps Man page Man page
mafByOverlaps,MafDb-method Man page
mafByOverlaps,MafDb2-method Man page
mafByOverlaps_nonsnvs Source code
mafByOverlaps_snvs Source code
matchSeqinfo Source code
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
normalizePath Source code
o_check_exists Source code
o_exists_mask Source code
onLoad Source code
organism,GenePhylostrataDb-method Man page
organism,MafDb-method Man page
organism,MafDb2-method Man page
param Man page
param,VariantFilteringResults-method Man page
plot,VariantFilteringResults,ANY-method Man page
populations Man page Man page
populations,MafDb-method Man page
populations,MafDb2-method Man page
ppath Source code
pprintseqs Source code
provider,MafDb-method Man page
provider,MafDb2-method Man page
providerVersion,MafDb-method Man page
providerVersion,MafDb2-method Man page
readAAradicalChangeMatrix Man page Source code
readPEDfile Source code
readWm Man page Source code
referenceGenome,MafDb-method Man page
referenceGenome,MafDb2-method Man page
reportVariants Man page
reportVariants,VariantFilteringResults-method Man page
resetSamples Man page
resetSamples,VariantFilteringResults-method Man page
sPkgLoaded Source code
samples Man page
samples,VariantFilteringResults-method Man page
samples<- Man page
samples<-,VariantFilteringResults,character-method Man page
samples<-,VariantFilteringResults-method Man page
scoreBindingSiteVariants Source code
scoreBindingSiteVariantsThisWM Source code
seqinfo,MafDb-method Man page
seqinfo,MafDb2-method Man page
seqlengths,MafDb-method Man page
seqlengths,MafDb2-method Man page
seqlevelsStyle,MafDb-method Man page
seqlevelsStyle,MafDb2-method Man page
seqnames,MafDb-method Man page
seqnames,MafDb2-method Man page
sequence_variant.gSOXP Man page
show,CompressedVRangesList-method Man page
show,FiveSpliceSiteVariants-method Man page
show,GenePhylostrataDb-method Man page
show,MafDb-method Man page
show,MafDb2-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
spliceSiteMatricesHuman Man page Source code
str2gr Source code Source code
strandedBamImport Source code
summary,VariantFilteringResults-method Man page
tabPanelAbout Source code
threeSpliceSites 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
xLinkedFilter Source code
xLinkedMask Source code
Bioconductor-mirror/VariantFiltering documentation built on Aug. 8, 2017, 5:45 a.m.