Fast Spatial Ancestry via Flexible Allele Frequency Surfaces

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Documentation for package ‘OriGen’ version 1.4.3

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OriGen-package Fast Spatial Ancestry via Flexible Allele Frequency Surfaces
10SNPs.map Plink sample PED data
10SNPs.ped Plink sample PED data
CalcFractionsMultiLoglik Calculates the loglikelihood for placing a sample 100 percent back into its own sample site
ConvertMicrosatData Microsatellite file conversion for known and unknown data
ConvertPEDData Plink PED file conversion
ConvertUnknownPEDData Plink PED file conversion for known and unknown data
FindRhoParameterCrossValidation Finds the appropriate value of the Rho parameter via crossvalidation.
FitAdmixedModelFindUnknowns Fit the OriGen model and place unknown individuals who may be admixed
FitMultinomialAdmixedModelFindUnknowns Fit the multinomial OriGen model and place unknown individuals who may be admixed
FitMultinomialModel Fit OriGen allele frequency surfaces
FitMultinomialModelFindUnknowns Fit OriGen microsatellite allele frequency surfaces
FitOriGenModel Fit OriGen allele frequency surfaces
FitOriGenModelFindUnknowns Fit the OriGen model and place unknown individuals
GenerateHeatMaps Fit OriGen microsatellite allele frequency surfaces
Locations Locations of individuals in 10SNPs
LocationsTrialDataSmall Locations of individuals in MicrosatTrialDataSmall
MicrosatTrialDataSmall Genotypes of individuals in located at LocationsTrialDataSmall
OriGen Fast Spatial Ancestry via Flexible Allele Frequency Surfaces
PlotAdmixedSurface Plots admixture fraction results
PlotAlleleFrequencySurface Plots an OriGen fitted allele frequency surface
PlotAlleleFrequencySurfaceOld Plots an OriGen fitted allele frequency surface
PlotUnknownHeatMap Plots a heat map depicting the probability an unknown individual comes from each block
RankSNPsLRT Rank the SNPs based on the likelihood ratio test.