A B C D E G H I M P R S T V misc
TVTB-package | TVTB: The VCF Tool Box |
aaf | TVTBparam class objects |
aaf-method | TVTBparam class objects |
aaf<- | TVTBparam class objects |
aaf<--method | TVTBparam class objects |
addCountGenos | Add count of genotypes to INFO field |
addCountGenos-method | Add count of genotypes to INFO field |
addCountGenos-methods | Add count of genotypes to INFO field |
addFrequencies | Group-level genotypes counts and allele frequencies |
addFrequencies-method | Group-level genotypes counts and allele frequencies |
addFrequencies-methods | Group-level genotypes counts and allele frequencies |
addOverallFrequencies | Overall genotypes counts and allele frequencies |
addOverallFrequencies-method | Overall genotypes counts and allele frequencies |
addOverallFrequencies-methods | Overall genotypes counts and allele frequencies |
addPhenoLevelFrequencies | Genotypes and allele frequencies for a given phenotype level |
addPhenoLevelFrequencies-method | Genotypes and allele frequencies for a given phenotype level |
addPhenoLevelFrequencies-methods | Genotypes and allele frequencies for a given phenotype level |
alt-method | Genotypes class objects |
alt-method | TVTBparam class objects |
alt<--method | Genotypes class objects |
alt<--method | TVTBparam class objects |
append-method | VCF filters class objects sub-types |
append-method | VcfFilterRules class objects |
autodetectGenotypes | Define genotypes in the TVTBparam metadata slot |
autodetectGenotypes-method | Define genotypes in the TVTBparam metadata slot |
autodetectGenotypes-methods | Define genotypes in the TVTBparam metadata slot |
bp | TVTBparam class objects |
bp-method | TVTBparam class objects |
bp<- | TVTBparam class objects |
bp<--method | TVTBparam class objects |
c-method | VCF filters class objects sub-types |
c-method | VcfFilterRules class objects |
carrier | Genotypes class objects |
carrier-method | Genotypes class objects |
carrier-method | TVTBparam class objects |
class:Genotypes | Genotypes class objects |
class:TVTBparam | TVTBparam class objects |
class:VcfFilterRules | VcfFilterRules class objects |
class:VcfFixedRules | VCF filters class objects sub-types |
class:VcfInfoRules | VCF filters class objects sub-types |
class:VcfVepRules | VCF filters class objects sub-types |
countGenos | Count occurences of genotypes |
countGenos-method | Count occurences of genotypes |
countGenos-methods | Count occurences of genotypes |
dropInfo | Remove INFO keys from VCF objects |
dropInfo-method | Remove INFO keys from VCF objects |
dropInfo-methods | Remove INFO keys from VCF objects |
eval-method | VCF filters class objects sub-types |
eval-method | VcfFilterRules class objects |
genos | Genotypes class objects |
genos-method | Genotypes class objects |
genos-method | TVTBparam class objects |
genos<- | TVTBparam class objects |
genos<--method | TVTBparam class objects |
Genotypes | Genotypes class objects |
Genotypes-class | Genotypes class objects |
Genotypes-methods | Genotypes class objects |
het | Genotypes class objects |
het-method | Genotypes class objects |
het-method | TVTBparam class objects |
het<- | Genotypes class objects |
het<--method | Genotypes class objects |
het<--method | TVTBparam class objects |
initialize-method | Genotypes class objects |
initialize-method | TVTBparam class objects |
initialize-method | VCF filters class objects sub-types |
initialize-method | VcfFilterRules class objects |
maf | TVTBparam class objects |
maf-method | TVTBparam class objects |
maf<- | TVTBparam class objects |
maf<--method | TVTBparam class objects |
pairsInfo | Plot an INFO metric on a genomic axis. |
pairsInfo-method | Plot an INFO metric on a genomic axis. |
pairsInfo-methods | Plot an INFO metric on a genomic axis. |
plotInfo | Plot an INFO metric on a genomic axis. |
plotInfo-method | Plot an INFO metric on a genomic axis. |
plotInfo-methods | Plot an INFO metric on a genomic axis. |
ranges | TVTBparam class objects |
ranges-method | TVTBparam class objects |
ranges<- | TVTBparam class objects |
ranges<--method | TVTBparam class objects |
readVcf-method | Read VCF files |
ref-method | Genotypes class objects |
ref-method | TVTBparam class objects |
ref<--method | Genotypes class objects |
ref<--method | TVTBparam class objects |
suffix | Genotypes class objects |
suffix-method | Genotypes class objects |
suffix-method | TVTBparam class objects |
svp | TVTBparam class objects |
svp-method | TVTBparam class objects |
svp<- | TVTBparam class objects |
svp<--method | TVTBparam class objects |
tSVE | The Shiny Variant Explorer (tSVE) web-application |
TVTBparam | TVTBparam class objects |
TVTBparam-class | TVTBparam class objects |
TVTBparam-methods | TVTBparam class objects |
type-method | VCF filters class objects sub-types |
type-method | VcfFilterRules class objects |
variantsInSamples | Identify variants observed in samples |
variantsInSamples-method | Identify variants observed in samples |
variantsInSamples-methods | Identify variants observed in samples |
VcfFilterRules | VcfFilterRules class objects |
VcfFilterRules-class | VcfFilterRules class objects |
VcfFixedRules | VCF filters class objects sub-types |
VcfFixedRules-class | VCF filters class objects sub-types |
VcfInfoRules | VCF filters class objects sub-types |
VcfInfoRules-class | VCF filters class objects sub-types |
VcfVepRules | VCF filters class objects sub-types |
VcfVepRules-class | VCF filters class objects sub-types |
vep | TVTBparam class objects |
vep-method | TVTBparam class objects |
vep-method | VCF filters class objects sub-types |
vep-method | VcfFilterRules class objects |
vep<- | TVTBparam class objects |
vep<--method | TVTBparam class objects |
vep<--method | VCF filters class objects sub-types |
vep<--method | VcfFilterRules class objects |
vepInPhenoLevel | VEP predictions of variants observed in samples |
vepInPhenoLevel-method | VEP predictions of variants observed in samples |
vepInPhenoLevel-methods | VEP predictions of variants observed in samples |
[-method | VCF filters class objects sub-types |
[-method | VcfFilterRules class objects |
[<--method | VCF filters class objects sub-types |
[<--method | VcfFilterRules class objects |
[[-method | VCF filters class objects sub-types |
[[-method | VcfFilterRules class objects |
[[<--method | VCF filters class objects sub-types |
[[<--method | VcfFilterRules class objects |