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VariantAnnotation (version 1.18.1)
Annotation of Genetic Variants
Description
Annotate variants, compute amino acid coding changes, predict coding outcomes.
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1.18.5
1.18.1
1.16.1
1.14.13
1.12.9
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Version
1.18.1
License
Artistic-2.0
Maintainer
Bioconductor Package Maintainer
Last Published
January 1st, 1970
Functions in VariantAnnotation (1.18.1)
Search functions
PolyPhenDb-class
PolyPhenDb objects
VRangesList-class
VRangesList objects
predictCoding
Predict amino acid coding changes for variants
locateVariants
Locate variants
filterVcf
Filter VCF files
scanVcf
Import VCF files
GLtoGP
Convert genotype likelihoods to genotype probabilities
genotypeToSnpMatrix
Convert genotype calls from a VCF file to a SnpMatrix object
VCF-class
VCF class objects
snpSummary
Counts and distribution statistics for SNPs in a VCF object
probabilityToSnpMatrix
Convert posterior genotype probability to a SnpMatrix object
writeVcf
Write VCF files
VariantAnnotation-defunct
Defunct Functions in Package
VariantAnnotation
summarizeVariants
Summarize variants by sample
SIFTDbColumns
SIFTDb Columns
SIFTDb-class
SIFTDb objects
readVcf
Read VCF files
VCFHeader-class
VCFHeader instances
getTranscriptSeqs
Get transcript sequences
PROVEANDb-class
PROVEANDb objects
ScanVcfParam-class
Parameters for scanning VCF files
VariantType-class
VariantType subclasses
VRanges-class
VRanges objects
PolyPhenDbColumns
PolyPhenDb Columns
isSNV
Identification of genomic variant types.