Fast Spatial Ancestry via Flexible Allele Frequency Surfaces

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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: 2013-10-13
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 function PlotAlleleFrequencySurface.

  • FitMultinomialModel Fits the OriGen model for microsatellites and returns the allele frequency surfaces. These surfaces can be plotted with the function PlotAlleleFrequencySurface.

  • 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 with PlotUnknownHeatMap. For microsatellite analysis see FitMultinomialModelFindUnknowns.

  • 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 with PlotUnknownHeatMap. For SNP analysis see FitOriGenModelFindUnknowns.

  • 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 function PlotAdmixedSurface.

  • 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 of FitOriGenModel or FitMultinomialModel. Note that all alleles can be plotted by setting AlleleNumber=0.

  • PlotUnknownHeatMap Plots a specified unknown individuals heat map from the output of FitOriGenModelFindUnknowns or FitMultinomialModelFindUnknowns.

  • PlotAdmixedSurface Plots the admixture fractions of a specified individual from the output of FitAdmixedModelFindUnknowns.

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):2915-22.

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