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

Global functions
$,VariantFilteringParam-method Man page
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
aMat2edgeList Source code
aaChangeType Man page
aaChangeType,VariantFilteringResults-method Man page
aaChangeType<- Man page
aaChangeType<-,VariantFilteringResults,character-method Man page
addSOmetadata Source code
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
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
browseVariants Man page Source code
buildAncestorsMatrix Source code
buildDescendantsMatrix Source code
cDNAloc Source code
change Man page
change<- Man page
change<-,CutoffsList,character-method Man page
change<-,CutoffsList,integer-method Man page
change<-,CutoffsList,logical-method Man page
change<-,CutoffsList,numeric-method Man page
checkValueCutoffArgs Source code
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
deNovoFilter Source code
deNovoMask 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
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
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
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
param Man page
param,VariantFilteringResults-method Man page
plot,VariantFilteringResults,ANY-method Man page
ppath Source code
readAAradicalChangeMatrix Man page Source code
readPEDfile 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
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
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
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
rcastelo/VariantFiltering documentation built on Dec. 13, 2017, 9:13 p.m.