OriGen: Fast Spatial Ancestry via Flexible Allele Frequency Surfaces

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.

Install the latest version of this package by entering the following in R:
install.packages("OriGen")
AuthorJohn Michael O Ranola, John Novembre, and Kenneth Lange
Date of publication2016-01-16 09:10:00
MaintainerJohn Michael O. Ranola <ranolaj@uw.edu>
LicenseGPL (>= 2)
Version1.4.3

View on CRAN

Man pages

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.

Functions

10SNPs.map Man page
10SNPs.ped Man page
CalcFractionsMultiLoglik Man page
ConvertMicrosatData Man page
ConvertPEDData Man page
ConvertUnknownPEDData Man page
FindRhoParameterCrossValidation Man page
FitAdmixedModelFindUnknowns Man page
FitMultinomialAdmixedModelFindUnknowns Man page
FitMultinomialModel Man page
FitMultinomialModelFindUnknowns Man page
FitOriGenModel Man page
FitOriGenModelFindUnknowns Man page
GenerateHeatMaps Man page
Locations Man page
LocationsTrialDataSmall Man page
MicrosatTrialDataSmall Man page
OriGen Man page
OriGen-package Man page
PlotAdmixedSurface Man page
PlotAlleleFrequencySurface Man page
PlotAlleleFrequencySurfaceOld Man page
PlotUnknownHeatMap Man page
RankSNPsLRT Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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