# Tools for variant data

## Documentation for package ‘SeqVarTools’ version 1.28.0

- 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