TVTB: The VCF Tool Box


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Documentation for package ‘TVTB’ version 1.4.0

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A B C D E G H I M P R S T V misc

TVTB-package TVTB: The VCF Tool Box

-- A --

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

-- B --

bp TVTBparam class objects
bp-method TVTBparam class objects
bp<- TVTBparam class objects
bp<--method TVTBparam class objects

-- C --

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

-- D --

dropInfo Remove INFO keys from VCF objects
dropInfo-method Remove INFO keys from VCF objects
dropInfo-methods Remove INFO keys from VCF objects

-- E --

eval-method VCF filters class objects sub-types
eval-method VcfFilterRules class objects

-- G --

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

-- H --

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

-- I --

initialize-method Genotypes class objects
initialize-method TVTBparam class objects
initialize-method VCF filters class objects sub-types
initialize-method VcfFilterRules class objects

-- M --

maf TVTBparam class objects
maf-method TVTBparam class objects
maf<- TVTBparam class objects
maf<--method TVTBparam class objects

-- P --

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.

-- R --

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

-- S --

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

-- T --

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

-- V --

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

-- misc --

[-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