Annotation of Genetic Variants


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Documentation for package ‘VariantAnnotation’ version 1.6.8

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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