Tools for variant data

---

Documentation for package ‘SeqVarTools’ version 1.42.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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