# Annotation of Genetic Variants

## Documentation for package ‘VariantAnnotation’ version 1.4.12

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

A C D 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 instances
alt-method | VCF instances
alt<- | VCF instances
alt<--method | VCF instances

## -- C --

class:PolyPhenDb | PolyPhenDb objects
class:SIFTDb | SIFTDb objects
class:VAFilter | VAFilter objects - under construction
CodingVariants | VariantType subclasses
CodingVariants-class | VariantType subclasses
cols-method | PolyPhenDb objects
cols-method | SIFTDb objects
compose | VAFilter objects - under construction
contig | VCFHeader instances
contig-method | VCFHeader instances

## -- D --

dbSNPFilter | VAFilter objects - under construction
downstream | VariantType subclasses
downstream-method | VariantType subclasses
downstream<- | VariantType subclasses
downstream<--method | VariantType subclasses
duplicateRSID | PolyPhenDb objects

## -- F --

filt | VCF instances
filt-method | VCF instances
filt<- | VCF instances
filt<--method | VCF instances
FiveUTRVariants | VariantType subclasses
FiveUTRVariants-class | VariantType subclasses
fixed | VCF instances
fixed-method | VCF instances
fixed-method | VCFHeader instances
fixed<- | VCF instances
fixed<--method | VCF instances

## -- G --

geno | VCF instances
geno-method | VCF instances
geno-method | VCFHeader instances
geno<- | VCF instances
geno<--method | VCF instances
genome-method | VCF instances
getTranscriptSeqs | Get transcript sequences
getTranscriptSeqs-method | Get transcript sequences

## -- H --

header | VCFHeader instances
header-method | VCFHeader instances

## -- I --

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

## -- K --

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

## -- L --

locateVariants | Locate variants
locateVariants-method | Locate variants
Logic-method | "VAFilterResult" for VAFilter output and statistics

## -- M --

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

## -- N --

name | VAFilter objects - under construction
name-method | VAFilter objects - under construction
name-method | "VAFilterResult" for VAFilter output and statistics

## -- 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
PromoterVariants | VariantType subclasses
PromoterVariants-class | VariantType subclasses

## -- Q --

qual | VCF instances
qual-method | VCF instances
qual<- | VCF instances
qual<--method | VCF instances

## -- R --

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 instances
ref-method | VCF instances
ref<- | VCF instances
ref<--method | VCF instances
reference | VCFHeader instances
reference-method | VCFHeader instances
refLocsToLocalLocs | refLocsToLocalLocs
refLocsToLocalLocs-method | refLocsToLocalLocs
regionFilter | VAFilter objects - under construction
renameSeqlevels-method | VCF instances

## -- 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 instances
show-method | VAFilter objects - under construction
show-method | "VAFilterResult" for VAFilter output and statistics
show-method | VCF instances
show-method | VCFHeader instances
show-method | VariantType subclasses
SIFT | SIFTDb objects
SIFTDb | SIFTDb objects
SIFTDb-class | SIFTDb objects
SIFTDbColumns | SIFTDb Columns
SpliceSiteVariants | VariantType subclasses
SpliceSiteVariants-class | VariantType subclasses
stats | "VAFilterResult" for VAFilter output and statistics
stats-method | "VAFilterResult" for VAFilter output and statistics
strand-method | VCF instances
strand<--method | VCF instances
summarizeVariants | Summarize variants by sample
summarizeVariants-method | Summarize variants by sample

## -- T --

ThreeUTRVariants | VariantType subclasses
ThreeUTRVariants-class | VariantType subclasses

## -- U --

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

## -- V --

VAFilter | VAFilter objects - under construction
vaFilter | VAFilter objects - under construction
VAFilter-class | VAFilter objects - under construction
vaFilter-method | VAFilter objects - under construction
VAFilterResult | "VAFilterResult" for VAFilter output and statistics
VAFilterResult-class | "VAFilterResult" for VAFilter output and statistics
VariantType-class | VariantType subclasses
VCF | VCF instances
VCF-class | VCF instances
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 | "VAFilterResult" for VAFilter output and statistics
.VAUtil-class | ".VAUtil" and potentially other related classes - in progress
[-method | VCF instances
[<--method | VCF instances