Man pages for smgogarten/SeqVarTools
Tools for variant data

alleleFrequencyAllele frequency
allele-methodsExtract allele information from a GDS object
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
meanBySampleMean value by sample
mendelErrMendelian errors
missingGenotypeRateMissing genotype rate
pcaPrincipal Component Analysis
pedigreePedigree for example data
refFracReference allele fraction
regressionLinear or logistic regression
SeqVarTools-packageTools for Variant Analysis
setVariantIDChange the variant ID of a GDS file
titvTransition/Transversion Ratio
variantInfoVariant info
smgogarten/SeqVarTools documentation built on Feb. 17, 2018, 4:25 a.m.