!-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 |