A C D E F G H I K L M P Q R S T U V W misc
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 |
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 |
downstream | VariantType subclasses |
downstream-method | VariantType subclasses |
downstream<- | VariantType subclasses |
downstream<--method | VariantType subclasses |
duplicateRSID | PolyPhenDb objects |
expand-method | VCF class objects |
ExpandedVCF | VCF class objects |
ExpandedVCF-class | VCF class 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 |
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 |
header | VCFHeader instances |
header-method | VCF class objects |
header-method | VCFHeader instances |
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 |
keepSeqlevels-method | VCF class objects |
keys-method | PolyPhenDb objects |
keys-method | SIFTDb objects |
locateVariants | Locate variants |
locateVariants-method | Locate variants |
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 |
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 |
qual | VCF class objects |
qual-method | VCF class objects |
qual<- | VCF class objects |
qual<--method | VCF class objects |
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 |
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 |
ThreeUTRVariants | VariantType subclasses |
ThreeUTRVariants-class | VariantType subclasses |
updateObject-method | VCF class objects |
upstream | VariantType subclasses |
upstream-method | VariantType subclasses |
upstream<- | VariantType subclasses |
upstream<--method | VariantType subclasses |
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 |
writeVcf | Write VCF files |
writeVcf-method | Write VCF files |
[-method | VCF class objects |
[<--method | VCF class objects |