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VariantAnnotation (version 1.18.5)

Annotation of Genetic Variants

Description

Annotate variants, compute amino acid coding changes, predict coding outcomes.

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Version

Version

1.18.5

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in VariantAnnotation (1.18.5)

VariantAnnotation-defunct

Defunct Functions in Package VariantAnnotation
isSNV

Identification of genomic variant types.
PolyPhenDb-class

PolyPhenDb objects
predictCoding

Predict amino acid coding changes for variants
PolyPhenDbColumns

PolyPhenDb Columns
filterVcf

Filter VCF files
genotypeToSnpMatrix

Convert genotype calls from a VCF file to a SnpMatrix object
getTranscriptSeqs

Get transcript sequences
locateVariants

Locate variants
GLtoGP

Convert genotype likelihoods to genotype probabilities
PROVEANDb-class

PROVEANDb objects
SIFTDbColumns

SIFTDb Columns
probabilityToSnpMatrix

Convert posterior genotype probability to a SnpMatrix object
readVcf

Read VCF files
snpSummary

Counts and distribution statistics for SNPs in a VCF object
scanVcf

Import VCF files
ScanVcfParam-class

Parameters for scanning VCF files
summarizeVariants

Summarize variants by sample
SIFTDb-class

SIFTDb objects
VariantType-class

VariantType subclasses
VcfFile

Manipulate Variant Call Format (Vcf) files.
VCF-class

VCF class objects
VCFHeader-class

VCFHeader instances
VRanges-class

VRanges objects
VRangesList-class

VRangesList objects
writeVcf

Write VCF files