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Version

Version

1.10.0

License

GPL-3

Maintainer

Stephanie M Gogarten

Last Published

February 15th, 2017

Functions in SeqVarTools (1.10.0)

duplicateDiscordance

Duplicate discordance
SeqVarData

SeqVarData
SeqVarTools-package

Tools for Variant Analysis
setVariantID

Change the variant ID of a GDS file
alternateAlleleDetection

alternateAlleleDetection
refFrac

Reference allele fraction
applyMethod

Apply method to GDS object
missingGenotypeRate

Missing genotype rate
isVariant

Locate variant samples across sites
alleleFrequency

Allele frequency
inbreedCoeff

Inbreeding coefficient
meanBySample

Mean value by sample
getGenotype

Get genotype data
pedigree

Pedigree for example data
pca

Principal Component Analysis
allele-methods

Extract allele information from a GDS object
hwe

Exact test for Hardy-Weinberg equilibrium
titv

Transition/Transversion Ratio
getVariableLengthData

Get variable-length data
heterozygosity

Heterozygosity and Homozygosity
isSNV

Flag single nucleotide variants
mendelErr

Mendelian errors
regression

Linear or logistic regression