# Annotation of Genetic Variants

## Documentation for package ‘VariantAnnotation’ version 1.40.0

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

## Help Pages

A C D E F G H I K L M N 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-method | VRanges objects
alt-method | VRangesList objects
alt<- | VCF class objects
alt<--method | VCF class objects
alt<--method | VRanges objects
altDepth | VRanges objects
altDepth-method | VRanges objects
altDepth<- | VRanges objects
altDepth<--method | VRanges objects
altFraction | VRanges objects
altFraction-method | VRanges objects
asVCF | VRanges objects
asVCF-method | VRanges objects

## -- C --

called | VRanges objects
called-method | VRanges objects
cbind-method | VCF class objects
characterOrRle-class | VRanges objects
characterRle-class | VRanges objects
class:CollapsedVCF | VCF class objects
class:CompressedVRangesList | VRangesList objects
class:ExpandedVCF | VCF class objects
class:PolyPhenDb | PolyPhenDb objects
class:PROVEANDb | PROVEANDb objects
class:SIFTDb | SIFTDb objects
class:SimpleVRangesList | VRangesList objects
class:VCF | VCF class objects
class:VRanges | VRanges objects
class:VRangesList | VRangesList objects
CodingVariants | VariantType subclasses
CodingVariants-class | VariantType subclasses
coerce-method | VRanges objects
CollapsedVCF | VCF class objects
CollapsedVCF-class | VCF class objects
columns-method | PROVEANDb objects
columns-method | PolyPhenDb objects
columns-method | SIFTDb objects
complexRle-class | VRanges objects
CompressedVRangesList-class | VRangesList objects
contig | VCFHeader instances
contig-method | VCFHeader instances

## -- D --

dbSNPFilter | Defunct Functions in Package 'VariantAnnotation'
dimnames<--method | VCF class objects
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 --

factorOrRle-class | VRanges objects
factorRle-class | VRanges objects
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
fixed<--method | VCFHeader instances

## -- G --

geno | VCF class objects
geno-method | VCF class objects
geno-method | VCFHeader instances
geno<- | VCF class objects
geno<--method | VCF class objects
geno<--method | VCFHeader instances
genome-method | VCF class objects
genotypeCodesToNucleotides | 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 --

hardFilters | VRanges objects
hardFilters-method | VRanges objects
hardFilters<- | VRanges objects
hardFilters<--method | VRanges objects
header | VCFHeader instances
header-method | VCF class objects
header-method | VCFHeader instances
header<- | VCF class objects
header<--method | VCF class objects

## -- I --

idType | VariantType subclasses
idType-method | VariantType subclasses
idType<- | VariantType subclasses
idType<--method | VariantType subclasses
import-method | Read VCF files
indexVcf | Create index files for VCF files
indexVcf-method | Create index files for VCF files
info | VCF class objects
info-method | VCF class objects
info-method | VCFHeader instances
info<- | VCF class objects
info<--method | VCF class objects
info<--method | VCFHeader instances
integerOrRle-class | VRanges objects
integerRle-class | VRanges objects
intergenic | VariantType subclasses
intergenic-method | VariantType subclasses
intergenic<- | VariantType subclasses
intergenic<--method | VariantType subclasses
IntergenicVariants | VariantType subclasses
IntergenicVariants-class | VariantType subclasses
IntronVariants | VariantType subclasses
IntronVariants-class | VariantType subclasses
isDeletion | Identification of genomic variant types.
isDeletion-method | Identification of genomic variant types.
isDelins | Identification of genomic variant types.
isDelins-method | Identification of genomic variant types.
isIndel | Identification of genomic variant types.
isIndel-method | Identification of genomic variant types.
isInsertion | Identification of genomic variant types.
isInsertion-method | Identification of genomic variant types.
isSNV | Identification of genomic variant types.
isSNV-method | Identification of genomic variant types.
isSubstitution | Identification of genomic variant types.
isSubstitution-method | Identification of genomic variant types.
isTransition | Identification of genomic variant types.
isTransition-method | Identification of genomic variant types.

## -- K --

keys-method | PROVEANDb objects
keys-method | PolyPhenDb objects
keys-method | SIFTDb objects
keytypes-method | PROVEANDb objects

## -- L --

locateVariants | Locate variants
locateVariants-method | Locate variants
logicalRle-class | VRanges objects

## -- M --

makeVRangesFromGRanges | VRanges objects
match-method | VRanges objects
MatrixToSnpMatrix | Defunct Functions in Package 'VariantAnnotation'
mcols<--method | VCF class objects
meta | VCFHeader instances
meta-method | VCFHeader instances
meta<- | VCFHeader instances
meta<--method | VCFHeader instances
metadata-method | PolyPhenDb objects
metadata-method | SIFTDb objects

## -- N --

numericRle-class | VRanges objects

## -- P --

PLtoGP | Convert genotype likelihoods to genotype probabilities
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
promoter | VariantType subclasses
promoter-method | VariantType subclasses
promoter<- | VariantType subclasses
promoter<--method | VariantType subclasses
PromoterVariants | VariantType subclasses
PromoterVariants-class | VariantType subclasses
PROVEAN | PROVEANDb objects
PROVEANDb | PROVEANDb objects
PROVEANDb-class | PROVEANDb objects

## -- Q --

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

## -- R --

rawRle-class | VRanges objects
rbind-method | VCF class objects
readGeno | Read VCF files
readGT | Read VCF files
readInfo | Read VCF files
readVcf | Read VCF files
readVcf-method | Read VCF files
readVcfAsVRanges | VRanges objects
readVcfLongForm | Defunct Functions in Package 'VariantAnnotation'
readVcfLongForm-method | Defunct Functions in Package 'VariantAnnotation'
ref | VCF class objects
ref-method | VCF class objects
ref-method | VRanges objects
ref-method | VRangesList objects
ref<- | VCF class objects
ref<--method | VCF class objects
ref<--method | VRanges objects
refDepth | VRanges objects
refDepth-method | VRanges objects
refDepth<- | VRanges objects
refDepth<--method | VRanges objects
reference | VCFHeader instances
reference-method | VCFHeader instances
refLocsToLocalLocs | Defunct Functions in Package 'VariantAnnotation'
refLocsToLocalLocs-method | Defunct Functions in Package 'VariantAnnotation'
regionFilter | Defunct Functions in Package 'VariantAnnotation'
resetFilter | VRanges objects
restrictToSNV | Defunct Functions in Package 'VariantAnnotation'
rowRanges-method | VCF class objects
rowRanges<--method | VCF class objects

## -- S --

sampleNames-method | VRanges objects
sampleNames<--method | VRanges objects
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 | PROVEANDb objects
select-method | PolyPhenDb objects
select-method | SIFTDb objects
seqinfo | Get seqinfo for VCF file
seqinfo-method | VCFHeader instances
seqinfo-method | Get seqinfo for VCF file
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
SimpleVRangesList-class | VRangesList objects
SnpMatrixToVCF | VCF class objects
snpSummary | Counts and distribution statistics for SNPs in a VCF object
snpSummary-method | Counts and distribution statistics for SNPs in a VCF object
softFilter | VRanges objects
softFilterMatrix | VRanges objects
softFilterMatrix-method | VRanges objects
softFilterMatrix<- | VRanges objects
softFilterMatrix<--method | VRanges objects
SpliceSiteVariants | VariantType subclasses
SpliceSiteVariants-class | VariantType subclasses
stackSamples | VRangesList objects
stackSamples-method | VRangesList objects
strand-method | VCF class objects
strand<--method | VCF class objects
subset-method | VCF class objects
summarizeVariants | Summarize variants by sample
summarizeVariants-method | Summarize variants by sample

## -- T --

tabulate | VRanges objects
tabulate-method | VRanges objects
ThreeUTRVariants | VariantType subclasses
ThreeUTRVariants-class | VariantType subclasses
totalDepth | VRanges objects
totalDepth-method | VRanges objects
totalDepth<- | VRanges objects
totalDepth<--method | VRanges objects

## -- U --

upstream | VariantType subclasses
upstream-method | VariantType subclasses
upstream<- | VariantType subclasses
upstream<--method | VariantType subclasses

## -- V --

VariantAnnotation-defunct | Defunct Functions in Package 'VariantAnnotation'
VariantType-class | VariantType subclasses
VCF | VCF class objects
VCF-class | VCF class objects
vcfFields | VCFHeader instances
vcfFields-method | VCF class objects
vcfFields-method | VCFHeader instances
vcfFields-method | Manipulate Variant Call Format (Vcf) files.
VcfFile | Manipulate Variant Call Format (Vcf) files.
VcfFile-class | Manipulate Variant Call Format (Vcf) files.
VcfFileList | Manipulate Variant Call Format (Vcf) files.
VcfFileList-class | Manipulate Variant Call Format (Vcf) files.
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
vcfSamples | Parameters for scanning VCF files
vcfSamples<- | 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
VRanges | VRanges objects
VRanges-class | VRanges objects
VRangesList | VRangesList objects
VRangesList-class | VRangesList objects
VRangesScanVcfParam | Defunct Functions in Package 'VariantAnnotation'

## -- W --

writeVcf | Write VCF files
writeVcf-method | VRanges objects
writeVcf-method | Write VCF files

## -- misc --

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