Package index

All functions

GLtoGP() PLtoGP()

Convert genotype likelihoods to genotype probabilities

PROVEAN PROVEANDb class:PROVEANDb PROVEANDb-class columns,PROVEANDb-method keys,PROVEANDb-method keytypes,PROVEANDb-method select,PROVEANDb-method

PROVEANDb objects

PolyPhen PolyPhenDb class:PolyPhenDb PolyPhenDb-class duplicateRSID metadata,PolyPhenDb-method columns,PolyPhenDb-method keys,PolyPhenDb-method select,PolyPhenDb-method

PolyPhenDb objects

PolyPhenDbColumns

PolyPhenDb Columns

SIFT SIFTDb class:SIFTDb SIFTDb-class metadata,SIFTDb-method columns,SIFTDb-method keys,SIFTDb-method select,SIFTDb-method

SIFTDb objects

SIFTDbColumns

SIFTDb Columns

ScanVcfParam() vcfFixed() `vcfFixed<-`() vcfInfo() `vcfInfo<-`() vcfGeno() `vcfGeno<-`() vcfSamples() `vcfSamples<-`() vcfTrimEmpty() `vcfTrimEmpty<-`() vcfWhich() `vcfWhich<-`()

Parameters for scanning VCF files

class:VCF VCF-class CollapsedVCF class:CollapsedVCF CollapsedVCF-class ExpandedVCF class:ExpandedVCF ExpandedVCF-class VCF SnpMatrixToVCF updateObject,VCF-method fixed fixed,VCF-method fixed<- fixed<-,VCF,DataFrame-method ref ref,VCF-method ref<- ref<-,VCF,DNAStringSet-method alt alt,VCF-method alt<- alt<-,CollapsedVCF,CharacterList-method alt<-,ExpandedVCF,character-method alt<-,CollapsedVCF,DNAStringSetList-method alt<-,ExpandedVCF,DNAStringSet-method qual qual,VCF-method qual<- qual<-,VCF,numeric-method filt filt,VCF-method filt<- filt<-,VCF,character-method info info,VCF-method info<- info<-,VCF,DataFrame-method rowRanges,VCF-method rowRanges<-,VCF,GRanges-method mcols<-,VCF-method mcols<-,VCF,ANY-method dimnames<-,VCF,list-method geno geno,VCF-method geno,VCF,ANY-method geno,VCF,character-method geno,VCF,numeric-method geno,VCFHeader,ANY-method geno<- geno<-,VCF,character,matrix-method geno<-,VCF,numeric,matrix-method geno<-,VCF,missing,matrix-method geno<-,VCF,missing,SimpleList-method strand,VCF-method strand<-,VCF,ANY-method header,VCF-method header<- header<-,VCF,VCFHeader-method vcfFields,VCF-method [,VCF-method [,VCF,ANY,ANY-method [,VCF,ANY,ANY,ANY-method subset,VCF-method [<-,VCF,ANY,ANY,VCF-method cbind,VCF-method rbind,VCF-method genome,VCF-method seqlevels,VCF-method expand,CollapsedVCF-method expand,ExpandedVCF-method genotypeCodesToNucleotides show,VCF-method show,CollapsedVCF-method show,ExpandedVCF-method

VCF class objects

VCFHeader-class VCFHeader reference reference,VCFHeader-method samples samples,VCFHeader-method header header,VCFHeader-method contig contig,VCFHeader-method meta meta,VCFHeader-method meta<- meta<-,VCFHeader,DataFrame-method meta<-,VCFHeader,DataFrameList-method fixed,VCFHeader-method fixed<-,VCFHeader,DataFrameList-method info,VCFHeader-method info<-,VCFHeader,DataFrame-method geno,VCFHeader-method geno<-,VCFHeader,missing,DataFrame-method seqinfo,VCFHeader-method vcfFields vcfFields,VCFHeader-method show,VCFHeader-method

VCFHeader instances

class:VRanges VRanges-class VRanges VRanges makeVRangesFromGRanges asVCF asVCF,VRanges-method coerce,VRanges,VCF-method coerce,VCF,VRanges-method coerce,GRanges,VRanges-method alt,VRanges-method alt<-,VRanges,ANY-method ref,VRanges-method ref<-,VRanges,ANY-method altDepth altDepth,VRanges-method altDepth<- altDepth<-,VRanges-method refDepth refDepth,VRanges-method refDepth<- refDepth<-,VRanges-method totalDepth totalDepth,VRanges-method totalDepth<- totalDepth<-,VRanges-method altFraction altFraction,VRanges-method called called,VRanges-method hardFilters<- hardFilters<-,VRanges-method hardFilters hardFilters,VRanges-method sampleNames,VRanges-method sampleNames<-,VRanges,ANY-method softFilterMatrix softFilterMatrix,VRanges-method softFilterMatrix<- softFilterMatrix<-,VRanges-method resetFilter tabulate tabulate,VRanges-method writeVcf,VRanges,ANY-method readVcfAsVRanges match,VRanges,VRanges-method softFilter characterRle-class characterOrRle-class complexRle-class factorRle-class factorOrRle-class integerRle-class integerOrRle-class logicalRle-class numericRle-class rawRle-class

VRanges objects

class:VRangesList VRangesList-class CompressedVRangesList-class class:CompressedVRangesList SimpleVRangesList-class class:SimpleVRangesList VRangesList alt,VRangesList-method ref,VRangesList-method stackSamples stackSamples,VRangesList-method

VRangesList objects

CodingVariants() IntronVariants() FiveUTRVariants() ThreeUTRVariants() SpliceSiteVariants() IntergenicVariants() PromoterVariants() AllVariants()

VariantType subclasses

VcfFile-class VcfFileList-class VcfFile VcfFileList vcfFields,missing-method vcfFields,character-method vcfFields,VcfFile-method vcfFields,VcfFileList-method

Manipulate Variant Call Format (Vcf) files.

VariantAnnotation-defunct refLocsToLocalLocs refLocsToLocalLocs,GRanges,TxDb,missing-method refLocsToLocalLocs,GRanges,missing,GRangesList-method readVcfLongForm readVcfLongForm,TabixFile,character,GRanges-method readVcfLongForm,TabixFile,character,missing-method readVcfLongForm,TabixFile,character,IntegerRangesList-method readVcfLongForm,TabixFile,character,ScanVcfParam-method readVcfLongForm,character,character,ScanVcfParam-method readVcfLongForm,character,character,missing-method readVcfLongForm,character,missing,missing-method dbSNPFilter regionFilter MatrixToSnpMatrix VRangesScanVcfParam restrictToSNV

Defunct Functions in Package VariantAnnotation

filterVcf(<character>) filterVcf(<TabixFile>)

Filter VCF files

genotypeToSnpMatrix(<CollapsedVCF>) genotypeToSnpMatrix(<array>)

Convert genotype calls from a VCF file to a SnpMatrix object

getTranscriptSeqs(<GRangesList>,<BSgenome>) getTranscriptSeqs(<GRangesList>,<FaFile>) getTranscriptSeqs(<GRanges>,<FaFile>)

Get transcript sequences

indexVcf(<character>) indexVcf(<VcfFile>) indexVcf(<VcfFileList>)

Create index files for VCF files

isSNV(<VRanges>) isSNV(<ExpandedVCF>) isSNV(<CollapsedVCF>) isInsertion(<VRanges>) isInsertion(<ExpandedVCF>) isInsertion(<CollapsedVCF>) isDeletion(<VRanges>) isDeletion(<ExpandedVCF>) isDeletion(<CollapsedVCF>) isIndel(<VRanges>) isIndel(<ExpandedVCF>) isIndel(<CollapsedVCF>) isDelins(<VRanges>) isDelins(<ExpandedVCF>) isDelins(<CollapsedVCF>) isTransition(<VRanges>) isTransition(<ExpandedVCF>) isTransition(<CollapsedVCF>) isSubstitution(<VRanges>) isSubstitution(<ExpandedVCF>) isSubstitution(<CollapsedVCF>)

Identification of genomic variant types.

locateVariants()

Locate variants

post_Hs_region()

elementary vep/homo_sapiens/region call to ensembl VEP REST API

predictCoding(<CollapsedVCF>,<TxDb>,<ANY>,<missing>) predictCoding(<ExpandedVCF>,<TxDb>,<ANY>,<missing>) predictCoding(<IntegerRanges>,<TxDb>,<ANY>,<DNAStringSet>) predictCoding(<GRanges>,<TxDb>,<ANY>,<DNAStringSet>) predictCoding(<VRanges>,<TxDb>,<ANY>,<missing>)

Predict amino acid coding changes for variants

probabilityToSnpMatrix()

Convert posterior genotype probability to a SnpMatrix object

readVcf(<TabixFile>,<ScanVcfParam>) readVcf(<TabixFile>,<IntegerRangesList>) readVcf(<TabixFile>,<GRanges>) readVcf(<TabixFile>,<GRangesList>) readVcf(<TabixFile>,<missing>) readVcf(<character>,<ANY>) readVcf(<character>,<missing>) readInfo() readGeno() readGT() import(<VcfFile>,<ANY>,<ANY>)

Read VCF files

run_vep()

Run a locally installed Ensembl VEP script on a VCF object or file

scanVcfHeader() scanVcf()

Import VCF files

seqinfo(<VcfFile>) seqinfo(<VcfFileList>)

Get seqinfo for VCF file

snpSummary(<CollapsedVCF>)

Counts and distribution statistics for SNPs in a VCF object

summarizeVariants(<TxDb>,<VCF>,<CodingVariants>) summarizeVariants(<TxDb>,<VCF>,<FiveUTRVariants>) summarizeVariants(<TxDb>,<VCF>,<ThreeUTRVariants>) summarizeVariants(<TxDb>,<VCF>,<SpliceSiteVariants>) summarizeVariants(<TxDb>,<VCF>,<IntronVariants>) summarizeVariants(<TxDb>,<VCF>,<PromoterVariants>) summarizeVariants(<GRangesList>,<VCF>,<VariantType>) summarizeVariants(<GRangesList>,<VCF>,<function>)

Summarize variants by sample

variant_body()

helper function to construct inputs for VEP REST API

vep_by_region()

Use the VEP region API on variant information in a VCF object as defined in VariantAnnotation.

writeVcf(<VCF>,<character>) writeVcf(<VCF>,<connection>)

Write VCF files