Annotation of Genetic Variants

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Documentation for package ‘VariantAnnotation’ version 1.4.12

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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