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