A C D F G H I K L M N P Q R S T V W misc
AllVariants | VariantType subclasses |
AllVariants-class | VariantType subclasses |
alt | VCF instances |
alt-method | VCF instances |
alt<- | VCF instances |
alt<--method | VCF instances |
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 |
dbSNPFilter | VAFilter objects - under construction |
duplicateRSID | PolyPhenDb objects |
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 |
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 |
globalToLocal | globalToLocal |
header | VCFHeader instances |
header-method | VCFHeader instances |
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 |
keepSeqlevels-method | VCF instances |
keys-method | PolyPhenDb objects |
keys-method | SIFTDb objects |
locateVariants | Locate variants |
locateVariants-method | Locate variants |
Logic-method | "VAFilterResult" for VAFilter output and statistics |
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 |
name | VAFilter objects - under construction |
name-method | VAFilter objects - under construction |
name-method | "VAFilterResult" for VAFilter output and statistics |
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 |
qual | VCF instances |
qual-method | VCF instances |
qual<- | VCF instances |
qual<--method | VCF instances |
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 |
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 |
ThreeUTRVariants | VariantType subclasses |
ThreeUTRVariants-class | VariantType subclasses |
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 |
vcfGeno | Parameters for scanning VCF files |
VCFHeader | VCFHeader instances |
VCFHeader-class | VCFHeader instances |
vcfInfo | Parameters for scanning VCF files |
vcfTrimEmpty | Parameters for scanning VCF files |
vcfWhich | Parameters for scanning VCF files |
writeVcf | Write VCF files |
writeVcf-method | Write VCF files |
!-method | "VAFilterResult" for VAFilter output and statistics |
.VAUtil-class | ".VAUtil" and potentially other related classes - in progress |
[-method | VCF instances |
[<--method | VCF instances |