Fast Spatial Ancestry via Flexible Allele Frequency Surfaces
Description
This package primarily estimates allele frequency surfaces from point estimates. It can also place individuals of unknown origin back onto the 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.
Details
Package:  OriGen 
Type:  Package 
Version:  0.1 
Date:  20131013 
License:  GPL2 
Index:

ConvertPEDData
This function converts Plink PED format files (PED/MAP) along with location files to the input required for OriGen. 
ConvertUnknownPEDData
This function converts Plink PED format files (PED/MAP) along with location files to the input required for OriGen. This differs from ConvertPEDData by its additional PED formatted input which contains the genotype information for unknown individuals. 
ConvertMicrosatData
This function converts Microsatellite data files into a format appropriate for analysis. 
FitOriGenModel
Fits the OriGen model for SNPs and returns the allele frequency surfaces. These surfaces can be plotted with the functionPlotAlleleFrequencySurface
. 
FitMultinomialModel
Fits the OriGen model for microsatellites and returns the allele frequency surfaces. These surfaces can be plotted with the functionPlotAlleleFrequencySurface
. 
FitOriGenModelFindUnknowns
Fits the OriGen model for SNPs and places individuals of unknown origin onto the map. This returns probability heat maps for each unknown individual. These heat maps can be plotted withPlotUnknownHeatMap
. For microsatellite analysis seeFitMultinomialModelFindUnknowns
. 
FitMultinomialModelFindUnknowns
Fits the OriGen model for microsatellites and places individuals of unknown origin onto the map. This returns probability heat maps for each unknown individual. These heat maps can be plotted withPlotUnknownHeatMap
. For SNP analysis seeFitOriGenModelFindUnknowns
. 
FitAdmixedModelFindUnknowns
Fits the OriGen model for SNPs and places unknown individuals who may be admixed onto the map. Instead of returning a probability heat map for each individual, this returns admixture fractions at each location. Note that many locations are 0. This can be plotted with the functionPlotAdmixedSurface
. 
RankSNPsLRT
This function takes a PED file along with a location file and outputs the likelihood ratio ranking of each SNP along with the LRT statistic and Rosenberg's informativeness for assignment. 
PlotAlleleFrequencySurface
Plots a specified allele frequency surface from the output ofFitOriGenModel
orFitMultinomialModel
. Note that all alleles can be plotted by setting AlleleNumber=0. 
PlotUnknownHeatMap
Plots a specified unknown individuals heat map from the output ofFitOriGenModelFindUnknowns
orFitMultinomialModelFindUnknowns
. 
PlotAdmixedSurface
Plots the admixture fractions of a specified individual from the output ofFitAdmixedModelFindUnknowns
.
Author(s)
John Michael Ranola, John Novembre, and Kenneth Lange
Maintainer: John Michael Ranola <ranolaj@uw.edu>
References
Ranola J, Novembre J, and Lange K (2014) Fast Spatial Ancestry via Flexible Allele Frequency Surfaces. Bioinformatics 30(20):291522.