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PlotUnknownHeatMap(HeatMapOutput,UnknownNumber=1,MaskWater=TRUE)
FitOriGenModelFindUnknowns
ConvertUnknownPEDData
for converting two Plink PED files (known and unknown)into a format appropriate for analysis,FitOriGenModelFindUnknowns
for fitting allele surfaces to the converted data and finding the locations of the given unknown individuals,
PlotUnknownHeatMap
for a quick way to plot the resulting unknown heat map surfaces from FitOriGenModelFindUnknowns
,
FitAdmixedModelFindUnknowns
for fitting allele surfaces to the converted data and finding the locations of the given unknown individuals who may be admixed,
PlotAdmixedSurface
for a quick way to plot the resulting admixture surfaces from FitAdmixedFindUnknowns
,
#this example not run because it takes slightly longer than 5 secs
#note - type example(FunctionName, run.dontrun=TRUE) to run the example where FunctionName is
#the name of the function
#Data generation
SampleSites=10
NumberSNPs=5
TestData=array(sample(2*(1:30),2*SampleSites*NumberSNPs,replace=TRUE),
dim=c(2,SampleSites,NumberSNPs))
#Europe is about -9 to 38 and 34 to 60
TestCoordinates=array(0,dim=c(SampleSites,2))
TestCoordinates[,1]=runif(SampleSites,-9,38)
TestCoordinates[,2]=runif(SampleSites,34,60)
#This code simulates the number of major alleles the unknown individuals have.
NumberUnknowns=2
TestUnknowns=array(sample(0:2,NumberUnknowns*NumberSNPs,replace=TRUE),
dim=c(NumberUnknowns,NumberSNPs))
#Fitting the model
#MaxGridLength is the maximum number of boxes allowed to span the region in either direction
#RhoParameter is a tuning constant
trials4=FitOriGenModelFindUnknowns(TestData,TestCoordinates,TestUnknowns,
MaxGridLength=20,RhoParameter=10)
str(trials4)
#Plotting the unknown heat map
PlotUnknownHeatMap(trials4,UnknownNumber=1,MaskWater=TRUE)
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