Annotation of Genetic Variants


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Documentation for package ‘VariantAnnotation’ version 1.0.5

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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