A B C D F G H I L M N O P R S T U V W X misc
| VariantFiltering-package | Filtering of coding and non-coding genetic variants |
| allVariants | VariantFilteringResults class |
| allVariants-method | VariantFilteringResults class |
| annoGroups | VariantFilteringResults class |
| annoGroups-method | VariantFilteringResults class |
| autosomalDominant | Autosomal dominant inheritance analysis |
| autosomalDominant-method | Autosomal dominant inheritance analysis |
| autosomalRecessiveHeterozygous | Autosomal recessive inheritance analysis: Heterozygous |
| autosomalRecessiveHeterozygous-method | Autosomal recessive inheritance analysis: Heterozygous |
| autosomalRecessiveHomozygous | Autosomal recessive inheritance analysis: Homozygous |
| autosomalRecessiveHomozygous-method | Autosomal recessive inheritance analysis: Homozygous |
| bamFiles | VariantFilteringResults class |
| bamFiles-method | VariantFilteringResults class |
| bamFiles<- | VariantFilteringResults class |
| bamFiles<--method | VariantFilteringResults class |
| browseVariants | VariantFilteringResults class |
| change | VariantFilteringResults class |
| change<- | VariantFilteringResults class |
| change<-,CutoffsList | VariantFilteringResults class |
| change<--method | VariantFilteringResults class |
| class:CutoffsList | VariantFilteringResults class |
| class:VariantFilteringParam | VariantFiltering parameter class |
| class:VariantFilteringResults | VariantFilteringResults class |
| conservedPositions | Weight matrix class |
| conservedPositions-method | Weight matrix class |
| cutoffs | VariantFilteringResults class |
| cutoffs-method | VariantFiltering parameter class |
| cutoffs-method | VariantFilteringResults class |
| cutoffs<- | VariantFilteringResults class |
| cutoffs<--method | VariantFilteringResults class |
| CutoffsList | VariantFilteringResults class |
| CutoffsList-class | VariantFilteringResults class |
| deNovo | De Novo variants analysis |
| deNovo-method | De Novo variants analysis |
| downstream | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| downstream-method | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| downstream<- | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| downstream<--method | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| filteredVariants | VariantFilteringResults class |
| filteredVariants-method | VariantFilteringResults class |
| filters | VariantFilteringResults class |
| filters-method | VariantFiltering parameter class |
| filters-method | VariantFilteringResults class |
| filters<- | VariantFilteringResults class |
| filters<--method | VariantFilteringResults class |
| filtersMetadata | VariantFilteringResults class |
| filtersMetadata-method | VariantFilteringResults class |
| FiveSpliceSiteVariants | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| FiveSpliceSiteVariants-class | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| genePhylostrata | PhastConsDb class |
| genePhylostrata-method | PhastConsDb class |
| GenePhylostrataDb | PhastConsDb class |
| GenePhylostrataDb-class | PhastConsDb class |
| genePhylostratum | PhastConsDb class |
| genePhylostratum-method | PhastConsDb class |
| humanGenesPhylostrata | PhastConsDb class |
| inheritanceModel | VariantFilteringResults class |
| inheritanceModel-method | VariantFilteringResults class |
| length | VariantFilteringResults class |
| length-method | VariantFilteringResults class |
| minIntronLength | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| minIntronLength-method | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| minIntronLength<- | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| minIntronLength<--method | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| names-method | VariantFiltering parameter class |
| organism-method | PhastConsDb class |
| param | VariantFilteringResults class |
| param-method | VariantFilteringResults class |
| plot-method | VariantFilteringResults class |
| readAAradicalChangeMatrix | Read matrix of amino acid radical changes |
| readWm | Weight matrix class |
| referenceGenome-method | VariantFilteringResults class |
| reportVariants | VariantFilteringResults class |
| reportVariants-method | VariantFilteringResults class |
| resetSamples | VariantFilteringResults class |
| resetSamples-method | VariantFilteringResults class |
| samples | VariantFilteringResults class |
| samples-method | VariantFilteringResults class |
| samples<- | VariantFilteringResults class |
| samples<--method | VariantFilteringResults class |
| sequence_variant.gSOXP | VariantFiltering parameter class |
| show-method | PhastConsDb class |
| show-method | VariantFiltering parameter class |
| show-method | VariantFilteringResults class |
| show-method | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| show-method | Weight matrix class |
| softFilterMatrix-method | VariantFilteringResults class |
| softFilterMatrix<--method | VariantFilteringResults class |
| sog | VariantFilteringResults class |
| sog-method | VariantFiltering parameter class |
| sog-method | VariantFilteringResults class |
| sortings | VariantFilteringResults class |
| sortings-method | VariantFilteringResults class |
| sortings<- | VariantFilteringResults class |
| sortings<--method | VariantFilteringResults class |
| spliceSiteMatricesHuman | VariantFiltering parameter class |
| summary-method | VariantFilteringResults class |
| ThreeSpliceSiteVariants | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| ThreeSpliceSiteVariants-class | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| unrelatedIndividuals | Analysis designed to be applied over a group of unrelated individuals |
| unrelatedIndividuals-method | Analysis designed to be applied over a group of unrelated individuals |
| upstream | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| upstream-method | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| upstream<- | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| upstream<--method | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
| VariantFiltering | Filtering of coding and non-coding genetic variants |
| VariantFilteringParam | VariantFiltering parameter class |
| VariantFilteringParam-class | VariantFiltering parameter class |
| VariantFilteringResults | VariantFilteringResults class |
| VariantFilteringResults-class | VariantFilteringResults class |
| variantLocations | VariantFiltering parameter class |
| WeightMatrix | Weight matrix class |
| WeightMatrix-class | Weight matrix class |
| width-method | Weight matrix class |
| wmFilename | Weight matrix class |
| wmFilename-method | Weight matrix class |
| wmLocations | Weight matrix class |
| wmLocations-method | Weight matrix class |
| wmLocations<- | Weight matrix class |
| wmLocations<--method | Weight matrix class |
| wmName | Weight matrix class |
| wmName-method | Weight matrix class |
| wmScore | Weight matrix class |
| wmScore-method | Weight matrix class |
| wmStrictLocations | Weight matrix class |
| wmStrictLocations-method | Weight matrix class |
| wmStrictLocations<- | Weight matrix class |
| wmStrictLocations<--method | Weight matrix class |
| xLinked | X-Linked inheritance analysis |
| xLinked-method | X-Linked inheritance analysis |
| $-method | VariantFiltering parameter class |