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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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Version

Version

1.14.13

License

Artistic-2.0

Maintainer

Valerie Obenchain

Last Published

February 15th, 2017

Functions in VariantAnnotation (1.14.13)

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