Package: |
OriGen |
Type: |
Package |
Version: |
0.1 |
Date: |
2013-10-13 |
License: |
GPL2 |
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
.