Man pages for smgogarten/SeqVarTools
Tools for variant data

alleleFrequencyAllele frequency
allele-methodsExtract allele information from a GDS object
alternateAlleleDetectionalternateAlleleDetection
applyMethodApply method to GDS object
chromWithPARIdentify pseudoautosomal region
countSingletonsCount singletons
duplicateDiscordanceDuplicate discordance
getGenotypeGet genotype data
getVariableLengthDataGet variable-length data
heterozygosityHeterozygosity and Homozygosity
hweExact test for Hardy-Weinberg equilibrium
inbreedCoeffInbreeding coefficient
isSNVFlag single nucleotide variants
isVariantLocate variant samples across sites
Iterator-classIterators
meanBySampleMean value by sample
mendelErrMendelian errors
missingGenotypeRateMissing genotype rate
pcaPrincipal Component Analysis
pedigreePedigree for example data
refFracReference allele fraction
regressionLinear or logistic regression
SeqVarData-classSeqVarData
SeqVarTools-packageTools for Variant Analysis
setVariantIDChange the variant ID of a GDS file
titvTransition/Transversion Ratio
variantInfoVariant info
smgogarten/SeqVarTools documentation built on Dec. 10, 2017, 6:28 p.m.