SeqVarData              SeqVarData
SeqVarIterator          Iterators
SeqVarTools-package     Tools for Variant Analysis
allele-methods          Extract allele information from a GDS object
alleleFrequency         Allele frequency
alternateAlleleDetection
                        alternateAlleleDetection
applyMethod             Apply method to GDS object
chromWithPAR            Identify pseudoautosomal region
countSingletons         Count singletons
duplicateDiscordance    Duplicate discordance
getGenotype             Get genotype data
getVariableLengthData   Get variable-length data
heterozygosity          Heterozygosity and Homozygosity
hwe                     Exact test for Hardy-Weinberg equilibrium
imputedDosage           Get imputed dosage
inbreedCoeff            Inbreeding coefficient
isSNV                   Flag single nucleotide variants
isVariant               Locate variant samples across sites
meanBySample            Mean value by sample
mendelErr               Mendelian errors
missingGenotypeRate     Missing genotype rate
pca                     Principal Component Analysis
pedigree                Pedigree for example data
refFrac                 Reference allele fraction
regression              Linear or logistic regression
setVariantID            Change the variant ID of a GDS file
titv                    Transition/Transversion Ratio
variantInfo             Variant info
