OriGen: Fast Spatial Ancestry via Flexible Allele Frequency Surfaces
Version 1.62

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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AuthorJohn Michael O Ranola, John Novembre, and Kenneth Lange
Date of publication2017-02-25 12:34:49
MaintainerJohn Michael O. Ranola <ranolaj@uw.edu>
LicenseGPL (>= 2)
Version1.62
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("OriGen", repos="http://R-Forge.R-project.org")

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 Source code
ConvertMicrosatData Man page Source code
ConvertPEDData Man page Source code
ConvertUnknownPEDData Man page Source code
FindRhoParameterCrossValidation Man page Source code
FitAdmixedModelFindUnknowns Man page Source code
FitMultinomialAdmixedModelFindUnknowns Man page Source code
FitMultinomialModel Man page Source code
FitMultinomialModelFindUnknowns Man page Source code
FitOriGenModel Man page Source code
FitOriGenModelFindUnknowns Man page Source code
GenerateHeatMaps Man page Source code
GenerateIsLandMatrix Source code
IsLand Source code
IsLandBool Source code
Locations Man page
LocationsTrialDataSmall Man page
MaskWater Source code
MicrosatTrialDataSmall Man page
OriGen Man page
OriGen-package Man page
PlotAdmixedSurface Man page Source code
PlotAlleleFrequencySurface Man page Source code
PlotAlleleFrequencySurfaceOld Man page Source code
PlotUnknownHeatMap Man page Source code
RankSNPsLRT Man page Source code
andArray Source code
s.wholenumber Source code

Files

DESCRIPTION
NAMESPACE
R
R/OriGen-internal.R
data
data/10SNPs.map.txt.gz
data/10SNPs.ped.txt.gz
data/Locations.txt.gz
data/LocationsTrialDataSmall.txt.gz
data/MicrosatTrialDataSmall.txt.gz
man
man/10SNPs.map.Rd
man/10SNPs.ped.Rd
man/CalcFractionsMultiLoglik.Rd
man/ConvertMicrosatData.Rd
man/ConvertPEDData.Rd
man/ConvertUnknownPEDData.Rd
man/FindRhoParameterCrossValidation.Rd
man/FitAdmixedModelFindUnknowns.Rd
man/FitMultinomialAdmixedModelFindUnknowns.Rd
man/FitMultinomialModel.Rd
man/FitMultinomialModelFindUnknowns.Rd
man/FitOriGenModel.Rd
man/FitOriGenModelFindUnknowns.Rd
man/GenerateHeatMaps.Rd
man/Locations.Rd
man/LocationsTrialDataSmall.Rd
man/MicrosatTrialDataSmall.Rd
man/OriGen-package.Rd
man/PlotAdmixedSurface.Rd
man/PlotAlleleFrequencySurface.Rd
man/PlotAlleleFrequencySurfaceOld.Rd
man/PlotUnknownHeatMap.Rd
man/RankSNPsLRT.Rd
src
src/OriGen.f90
OriGen documentation built on May 21, 2017, 2:51 a.m.