# Tools for variant data

## Documentation for package ‘SeqVarTools’ version 1.12.0

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

## Help Pages

SeqVarTools-package | Tools for Variant Analysis
allele-methods | Extract allele information from a GDS object
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
countSingletons | Count singletons
countSingletons-method | Count singletons
duplicateDiscordance | Duplicate discordance
duplicateDiscordance-method | Duplicate discordance
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
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
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
meanBySample | Mean value by sample
meanBySample-method | Mean value by sample
mendelErr | Mendelian errors
mendelErr-method | Mendelian errors
missingGenotypeRate | Missing genotype rate
missingGenotypeRate-method | Missing genotype rate
nAlleles | Extract allele information from a GDS object
nAlleles-method | Extract allele information from a GDS object
pca | Principal Component Analysis
pca-method | Principal Component Analysis
pedigree | Pedigree for example data
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
sampleData | SeqVarData
sampleData-method | SeqVarData
sampleData<- | SeqVarData
sampleData<--method | SeqVarData
SeqVarData | SeqVarData
SeqVarData-class | SeqVarData
SeqVarTools | Tools for Variant Analysis
setVariantID | Change the variant ID of a GDS file
titv | Transition/Transversion Ratio
titv-method | Transition/Transversion Ratio
variantData | SeqVarData
variantData-method | SeqVarData
variantData<- | SeqVarData
variantData<--method | SeqVarData