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.
|Author||John Michael O Ranola, John Novembre, and Kenneth Lange|
|Date of publication||2016-01-16 09:10:00|
|Maintainer||John Michael O. Ranola <email@example.com>|
|License||GPL (>= 2)|
10SNPs.map: Plink sample PED data
10SNPs.ped: Plink sample PED data
CalcFractionsMultiLoglik: Calculates the loglikelihood for placing a sample 100 percent...
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...
FitAdmixedModelFindUnknowns: Fit the OriGen model and place unknown individuals who may be...
FitMultinomialAdmixedModelFindUnknowns: Fit the multinomial OriGen model and place unknown...
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...
OriGen-package: 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...
RankSNPsLRT: Rank the SNPs based on the likelihood ratio test.