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OriGen (version 1.4.3)

Fast Spatial Ancestry via Flexible Allele Frequency Surfaces

Description

Used primarily for estimates of allele frequency surfaces from point estimates. It can also place individuals of unknown origin back onto the geographic map with great accuracy. Additionally, it can place admixed individuals by estimating contributing fractions at each location on a map. Lastly, it can rank SNPs by their ability to differentiate populations. See "Fast Spatial Ancestry via Flexible Allele Frequency Surfaces" (John Michael Ranola, John Novembre, Kenneth Lange) in Bioinformatics 2014 for more info.

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Version

Install

install.packages('OriGen')

Monthly Downloads

26

Version

1.4.3

License

GPL (>= 2)

Maintainer

John Michael O Ranola

Last Published

January 16th, 2016

Functions in OriGen (1.4.3)

Locations

Locations of individuals in 10SNPs
ConvertMicrosatData

Microsatellite file conversion for known and unknown data
GenerateHeatMaps

Fit OriGen microsatellite allele frequency surfaces
RankSNPsLRT

Rank the SNPs based on the likelihood ratio test.
MicrosatTrialDataSmall

Genotypes of individuals in located at LocationsTrialDataSmall
LocationsTrialDataSmall

Locations of individuals in MicrosatTrialDataSmall
10SNPs.ped

Plink sample PED data
FindRhoParameterCrossValidation

Finds the appropriate value of the Rho parameter via crossvalidation.
ConvertUnknownPEDData

Plink PED file conversion for known and unknown data
ConvertPEDData

Plink PED file conversion
FitOriGenModel

Fit OriGen allele frequency surfaces
PlotAlleleFrequencySurface

Plots an OriGen fitted allele frequency surface
FitMultinomialModel

Fit OriGen allele frequency surfaces
FitMultinomialModelFindUnknowns

Fit OriGen microsatellite allele frequency surfaces
OriGen-package

Fast Spatial Ancestry via Flexible Allele Frequency Surfaces
10SNPs.map

Plink sample PED data
PlotAlleleFrequencySurfaceOld

Plots an OriGen fitted allele frequency surface
CalcFractionsMultiLoglik

Calculates the loglikelihood for placing a sample 100 percent back into its own sample site
PlotAdmixedSurface

Plots admixture fraction results
FitMultinomialAdmixedModelFindUnknowns

Fit the multinomial OriGen model and place unknown individuals who may be admixed
FitOriGenModelFindUnknowns

Fit the OriGen model and place unknown individuals
PlotUnknownHeatMap

Plots a heat map depicting the probability an unknown individual comes from each block
FitAdmixedModelFindUnknowns

Fit the OriGen model and place unknown individuals who may be admixed