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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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Version

Version

1.18.1

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in VariantAnnotation (1.18.1)

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.