Annotation of Genetic Variants
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘VariantAnnotation’ version 1.44.0
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 |