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| !-method | "VAFilterResult" for VAFilter output and statistics |
| .VAUtil-class | ".VAUtil" and potentially other related classes - in progress |
| c-method | "VAFilter" for representing functions operating on genetic variants |
| class:PolyPhenDb | PolyPhenDb objects |
| class:SIFTDb | SIFTDb objects |
| coerce-method | "VAFilter" for representing functions operating on genetic variants |
| cols-method | PolyPhenDb objects |
| cols-method | SIFTDb objects |
| compose | Functions for VariantAnnotation filters |
| dbSNPFilter | Functions for VariantAnnotation filters |
| duplicateRSID | PolyPhenDb objects |
| getTranscriptSeqs | Get transcript sequences |
| getTranscriptSeqs-method | Get transcript sequences |
| globalToLocal | globalToLocal |
| keys-method | PolyPhenDb objects |
| keys-method | SIFTDb objects |
| locateVariants | Locate variants |
| locateVariants-method | Locate variants |
| Logic-method | "VAFilterResult" for VAFilter output and statistics |
| MatrixToSnpMatrix | Convert a matrix of genotype calls to a SnpMatrix object |
| metadata-method | PolyPhenDb objects |
| metadata-method | SIFTDb objects |
| name | "VAFilter" for representing functions operating on genetic variants |
| name-method | "VAFilter" for representing functions operating on genetic variants |
| name-method | "VAFilterResult" for VAFilter output and statistics |
| PolyPhen | PolyPhenDb objects |
| PolyPhenDb | PolyPhenDb objects |
| PolyPhenDb-class | PolyPhenDb objects |
| PolyPhenDbColumns | PolyPhenDb Columns |
| predictCoding | Predict amino acid coding changes for variants |
| predictCoding-method | Predict amino acid coding changes for variants |
| readVcf | Read VCF (variant call format) files into a SummarizedExperiment object |
| readVcf-method | Read VCF (variant call format) files into a SummarizedExperiment object |
| regionFilter | Functions for VariantAnnotation filters |
| select-method | PolyPhenDb objects |
| select-method | SIFTDb objects |
| show-method | "VAFilter" for representing functions operating on genetic variants |
| show-method | "VAFilterResult" for VAFilter output and statistics |
| SIFT | SIFTDb objects |
| SIFTDb | SIFTDb objects |
| SIFTDb-class | SIFTDb objects |
| SIFTDbColumns | SIFTDb Columns |
| stats | "VAFilterResult" for VAFilter output and statistics |
| stats-method | "VAFilterResult" for VAFilter output and statistics |
| vaFilter | Functions for VariantAnnotation filters |
| VAFilter-class | "VAFilter" for representing functions operating on genetic variants |
| vaFilter-method | "VAFilter" for representing functions operating on genetic variants |
| vaFilter-method | Functions for VariantAnnotation filters |
| VAFilterResult | "VAFilterResult" for VAFilter output and statistics |
| VAFilterResult-class | "VAFilterResult" for VAFilter output and statistics |
| variants | Human genetic variant test dataset |