Tools for variant data


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Documentation for package ‘SeqVarTools’ version 1.25.0

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A C D E G H I L M N P R S T V

SeqVarTools-package Tools for Variant Analysis

-- A --

allele-methods Extract allele information from a GDS object
alleleCount Allele frequency
alleleCount-method Allele frequency
alleleDosage Get genotype data
alleleDosage-method Get genotype data
alleleFrequency Allele frequency
alleleFrequency-method Allele frequency
altChar Extract allele information from a GDS object
altChar-method Extract allele information from a GDS object
altDosage Get genotype data
altDosage-method Get genotype data
alternateAlleleDetection alternateAlleleDetection
alternateAlleleDetection-method alternateAlleleDetection
applyMethod Apply method to GDS object
applyMethod-method Apply method to GDS object

-- C --

chromWithPAR Identify pseudoautosomal region
chromWithPAR-method Identify pseudoautosomal region
countSingletons Count singletons
countSingletons-method Count singletons
currentRanges Iterators
currentRanges-method Iterators
currentVariants Iterators
currentVariants-method Iterators

-- D --

duplicateDiscordance Duplicate discordance
duplicateDiscordance-method Duplicate discordance

-- E --

expandedAltDosage Get genotype data
expandedAltDosage-method Get genotype data
expandedVariantIndex Variant info
expandedVariantIndex-method Variant info

-- G --

getGenotype Get genotype data
getGenotype-method Get genotype data
getGenotypeAlleles Get genotype data
getGenotypeAlleles-method Get genotype data
getVariableLengthData Get variable-length data
getVariableLengthData-method Get variable-length data
granges SeqVarData
granges-method SeqVarData

-- H --

heterozygosity Heterozygosity and Homozygosity
heterozygosity-method Heterozygosity and Homozygosity
hethom Heterozygosity and Homozygosity
hethom-method Heterozygosity and Homozygosity
homozygosity Heterozygosity and Homozygosity
homozygosity-method Heterozygosity and Homozygosity
hwe Exact test for Hardy-Weinberg equilibrium
hwe-method Exact test for Hardy-Weinberg equilibrium

-- I --

imputedDosage Get imputed dosage
imputedDosage-method Get imputed dosage
inbreedCoeff Inbreeding coefficient
inbreedCoeff-method Inbreeding coefficient
isSNV Flag single nucleotide variants
isSNV-method Flag single nucleotide variants
isVariant Locate variant samples across sites
isVariant-method Locate variant samples across sites
iterateFilter Iterators
iterateFilter-method Iterators

-- L --

lastFilter Iterators
lastFilter-method Iterators
lastFilter<- Iterators
lastFilter<--method Iterators

-- M --

meanBySample Mean value by sample
meanBySample-method Mean value by sample
mendelErr Mendelian errors
mendelErr-method Mendelian errors
minorAlleleCount Allele frequency
minorAlleleCount-method Allele frequency
missingGenotypeRate Missing genotype rate
missingGenotypeRate-method Missing genotype rate

-- N --

nAlleles Extract allele information from a GDS object
nAlleles-method Extract allele information from a GDS object

-- P --

pca Principal Component Analysis
pca-method Principal Component Analysis
pedigree Pedigree for example data

-- R --

refChar Extract allele information from a GDS object
refChar-method Extract allele information from a GDS object
refDosage Get genotype data
refDosage-method Get genotype data
refFrac Reference allele fraction
refFrac-method Reference allele fraction
refFracOverHets Reference allele fraction
refFracOverHets-method Reference allele fraction
refFracPlot Reference allele fraction
refFracPlot-method Reference allele fraction
regression Linear or logistic regression
regression-method Linear or logistic regression
resetIterator Iterators
resetIterator-method Iterators

-- S --

sampleData SeqVarData
sampleData-method SeqVarData
sampleData<- SeqVarData
sampleData<--method SeqVarData
SeqVarBlockIterator Iterators
SeqVarBlockIterator-class Iterators
SeqVarData SeqVarData
SeqVarData-class SeqVarData
SeqVarIterator Iterators
SeqVarIterator-class Iterators
SeqVarListIterator Iterators
SeqVarListIterator-class Iterators
SeqVarRangeIterator Iterators
SeqVarRangeIterator-class Iterators
SeqVarTools Tools for Variant Analysis
SeqVarWindowIterator Iterators
SeqVarWindowIterator-class Iterators
setVariantID Change the variant ID of a GDS file
show-method Iterators
show-method SeqVarData

-- T --

titv Transition/Transversion Ratio
titv-method Transition/Transversion Ratio

-- V --

validateSex SeqVarData
validateSex-method SeqVarData
variantBlock Iterators
variantBlock-method Iterators
variantData SeqVarData
variantData-method SeqVarData
variantData<- SeqVarData
variantData<--method SeqVarData
variantFilter Iterators
variantFilter-method Iterators
variantInfo Variant info
variantInfo-method Variant info
variantRanges Iterators
variantRanges-method Iterators