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.

Author
John Michael O Ranola, John Novembre, and Kenneth Lange
Date of publication
2016-01-16 09:10:00
Maintainer
John Michael O. Ranola <ranolaj@uw.edu>
License
GPL (>= 2)
Version
1.4.3

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.

Files in this package

OriGen
OriGen/src
OriGen/src/OriGen.f90
OriGen/NAMESPACE
OriGen/data
OriGen/data/LocationsTrialDataSmall.txt.gz
OriGen/data/10SNPs.map.txt.gz
OriGen/data/Locations.txt.gz
OriGen/data/MicrosatTrialDataSmall.txt.gz
OriGen/data/10SNPs.ped.txt.gz
OriGen/R
OriGen/R/OriGen-internal.R
OriGen/MD5
OriGen/DESCRIPTION
OriGen/man
OriGen/man/Locations.Rd
OriGen/man/FitMultinomialModelFindUnknowns.Rd
OriGen/man/10SNPs.map.Rd
OriGen/man/FitOriGenModelFindUnknowns.Rd
OriGen/man/RankSNPsLRT.Rd
OriGen/man/OriGen-package.Rd
OriGen/man/PlotUnknownHeatMap.Rd
OriGen/man/ConvertMicrosatData.Rd
OriGen/man/10SNPs.ped.Rd
OriGen/man/MicrosatTrialDataSmall.Rd
OriGen/man/PlotAlleleFrequencySurface.Rd
OriGen/man/FindRhoParameterCrossValidation.Rd
OriGen/man/FitAdmixedModelFindUnknowns.Rd
OriGen/man/LocationsTrialDataSmall.Rd
OriGen/man/ConvertUnknownPEDData.Rd
OriGen/man/FitOriGenModel.Rd
OriGen/man/ConvertPEDData.Rd
OriGen/man/PlotAdmixedSurface.Rd
OriGen/man/FitMultinomialModel.Rd
OriGen/man/PlotAlleleFrequencySurfaceOld.Rd
OriGen/man/FitMultinomialAdmixedModelFindUnknowns.Rd
OriGen/man/GenerateHeatMaps.Rd
OriGen/man/CalcFractionsMultiLoglik.Rd