# Annotation of Genetic Variants

## Documentation for package ‘VariantAnnotation’ version 1.6.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G H I K L M P Q R S T U V W misc

## -- A --

AllVariants | VariantType subclasses
AllVariants-class | VariantType subclasses
alt | VCF class objects
alt-method | VCF class objects
alt<- | VCF class objects
alt<--method | VCF class objects

## -- C --

cbind-method | VCF class objects
class:CollapsedVCF | VCF class objects
class:ExpandedVCF | VCF class objects
class:PolyPhenDb | PolyPhenDb objects
class:SIFTDb | SIFTDb objects
class:VCF | VCF class objects
CodingVariants | VariantType subclasses
CodingVariants-class | VariantType subclasses
CollapsedVCF | VCF class objects
CollapsedVCF-class | VCF class objects
cols-method | PolyPhenDb objects
cols-method | SIFTDb objects
contig | VCFHeader instances
contig-method | VCFHeader instances

## -- D --

downstream | VariantType subclasses
downstream-method | VariantType subclasses
downstream<- | VariantType subclasses
downstream<--method | VariantType subclasses
duplicateRSID | PolyPhenDb objects

## -- E --

expand-method | VCF class objects
ExpandedVCF | VCF class objects
ExpandedVCF-class | VCF class objects

## -- F --

filt | VCF class objects
filt-method | VCF class objects
filt<- | VCF class objects
filt<--method | VCF class objects
filterVcf | Filter VCF files
filterVcf-method | Filter VCF files
FiveUTRVariants | VariantType subclasses
FiveUTRVariants-class | VariantType subclasses
fixed | VCF class objects
fixed-method | VCF class objects
fixed-method | VCFHeader instances
fixed<- | VCF class objects
fixed<--method | VCF class objects

## -- G --

geno | VCF class objects
geno-method | VCF class objects
geno-method | VCFHeader instances
geno<- | VCF class objects
geno<--method | VCF class objects
genome-method | VCF class objects
genotypeToSnpMatrix | Convert genotype calls from a VCF file to a SnpMatrix object
genotypeToSnpMatrix-method | Convert genotype calls from a VCF file to a SnpMatrix object
getTranscriptSeqs | Get transcript sequences
getTranscriptSeqs-method | Get transcript sequences
GLtoGP | Convert genotype likelihoods to genotype probabilities

## -- H --

header | VCFHeader instances
header-method | VCF class objects
header-method | VCFHeader instances

## -- I --

info | VCF class objects
info-method | VCF class objects
info-method | VCFHeader instances
info<- | VCF class objects
info<--method | VCF class objects
IntergenicVariants | VariantType subclasses
IntergenicVariants-class | VariantType subclasses
IntronVariants | VariantType subclasses
IntronVariants-class | VariantType subclasses

## -- K --

keepSeqlevels-method | VCF class objects
keys-method | PolyPhenDb objects
keys-method | SIFTDb objects

## -- L --

locateVariants | Locate variants
locateVariants-method | Locate variants

## -- M --

MatrixToSnpMatrix | Convert genotype calls from a VCF file to a SnpMatrix object
MatrixToSnpMatrix-deprecated | Convert genotype calls from a VCF file to a SnpMatrix object
MatrixToSnpMatrix-method | Convert genotype calls from a VCF file to a SnpMatrix object
mcols<--method | VCF class objects
meta | VCFHeader instances
meta-method | VCFHeader instances
metadata-method | PolyPhenDb objects
metadata-method | SIFTDb objects

## -- P --

PolyPhen | PolyPhenDb objects
PolyPhenDb | PolyPhenDb objects
PolyPhenDb-class | PolyPhenDb objects
PolyPhenDbColumns | PolyPhenDb Columns
predictCoding | Predict amino acid coding changes for variants
predictCoding-method | Predict amino acid coding changes for variants
probabilityToSnpMatrix | Convert posterior genotype probability to a SnpMatrix object
PromoterVariants | VariantType subclasses
PromoterVariants-class | VariantType subclasses

## -- Q --

qual | VCF class objects
qual-method | VCF class objects
qual<- | VCF class objects
qual<--method | VCF class objects

## -- R --

rbind-method | VCF class objects
readVcf | Read VCF files
readVcf-method | Read VCF files
readVcfLongForm | Read VCF files into a long form GRanges
readVcfLongForm-method | Read VCF files into a long form GRanges
ref | VCF class objects
ref-method | VCF class objects
ref<- | VCF class objects
ref<--method | VCF class objects
reference | VCFHeader instances
reference-method | VCFHeader instances
refLocsToLocalLocs | refLocsToLocalLocs
refLocsToLocalLocs-method | refLocsToLocalLocs
renameSeqlevels-method | VCF class objects
rowData-method | VCF class objects
rowData<--method | VCF class objects

## -- S --

samples | VCFHeader instances
samples-method | VCFHeader instances
scanVcf | Import VCF files
scanVcf-method | Import VCF files
scanVcfHeader | Import VCF files
scanVcfHeader-method | Import VCF files
ScanVcfParam | Parameters for scanning VCF files
ScanVcfParam-class | Parameters for scanning VCF files
ScanVcfParam-method | Parameters for scanning VCF files
select-method | PolyPhenDb objects
select-method | SIFTDb objects
seqlevels-method | VCF class objects
show-method | VCF class objects
show-method | VCFHeader instances
show-method | VariantType subclasses
SIFT | SIFTDb objects
SIFTDb | SIFTDb objects
SIFTDb-class | SIFTDb objects
SIFTDbColumns | SIFTDb Columns
snpSummary | Counts and distribution statistics for SNPs in a VCF object
snpSummary-method | Counts and distribution statistics for SNPs in a VCF object
SpliceSiteVariants | VariantType subclasses
SpliceSiteVariants-class | VariantType subclasses
strand-method | VCF class objects
strand<--method | VCF class objects
summarizeVariants | Summarize variants by sample
summarizeVariants-method | Summarize variants by sample

## -- T --

ThreeUTRVariants | VariantType subclasses
ThreeUTRVariants-class | VariantType subclasses

## -- U --

updateObject-method | VCF class objects
upstream | VariantType subclasses
upstream-method | VariantType subclasses
upstream<- | VariantType subclasses
upstream<--method | VariantType subclasses

## -- V --

VariantType-class | VariantType subclasses
VCF | VCF class objects
VCF-class | VCF class objects
vcfFixed | Parameters for scanning VCF files
vcfFixed<- | Parameters for scanning VCF files
vcfGeno | Parameters for scanning VCF files
vcfGeno<- | Parameters for scanning VCF files
VCFHeader | VCFHeader instances
VCFHeader-class | VCFHeader instances
vcfInfo | Parameters for scanning VCF files
vcfInfo<- | Parameters for scanning VCF files
vcfTrimEmpty | Parameters for scanning VCF files
vcfTrimEmpty<- | Parameters for scanning VCF files
vcfWhich | Parameters for scanning VCF files
vcfWhich<- | Parameters for scanning VCF files

## -- W --

writeVcf | Write VCF files
writeVcf-method | Write VCF files

## -- misc --

[-method | VCF class objects
[<--method | VCF class objects