Fit OriGen allele frequency surfaces

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Description

This function fits allele frequency surfaces to the data.

Usage

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FitOriGenModel(DataArray,SampleCoordinates,MaxGridLength=20,RhoParameter=10)

Arguments

DataArray

An array giving the number of major/minor SNPs (defined as the most occuring in the dataset) grouped by sample sites for each SNP. The dimension of this array is [2,SampleSites,NumberSNPs].

SampleCoordinates

This is an array which gives the longitude and latitude of each of the found sample sites. The dimension of this array is [SampleSites,2], where the second dimension represents longitude and latitude respectively.

MaxGridLength

An integer giving the maximum number of boxes to fill the longer side of the region. Note that computation time increases quadratically as this number increases, but this number also should be high enough to separate different sample sites otherwise they will be binned together as a single site.

RhoParameter

This is a real precision parameter weighting the amount of smoothing. A higher value flattens out the surface while a lower value allows for more fluctuations. The default value of 10 was used in our analysis and should prove a good starting point. To choose a value by crossvalidation please see FindRhoParameterCrossValidation

Value

List with the following components:

AlleleFrequencySurfaces

An array giving the allele frequency for each coordinate and each SNP. The dimension of this array is [NumberSNPs, NumberLongitudeDivisions, NumberLatitudeDivisions], where either NumberLongitudeDivisions or NumberLatitudeDivisions is equal to MaxGridLength(an input to this function) and the other is scaled so that the geodesic distance between points horizontally and vertically is equal.

DataArray

An array giving the number of major/minor SNPs (defined as the most occuring in the dataset) grouped by sample sites for each SNP. The dimension of this array is [2,SampleSites,NumberSNPs].

NumberSNPs

This shows the integer number of SNPs found.

GridLength

An array giving the number of longitudinal and latitudinal divisions. The dimension of this array is [2], where the first number is longitude and the second is latitude.

RhoParameter

A real value showing the inputted RhoParameter value.

SampleSites

This shows the integer number of sample sites found.

MaxGridLength

An integer giving the maximum number of boxes to fill the longer side of the region. Note that computation time increases quadratically as this number increases, but this number also should be high enough to separate different sample sites otherwise they will be binned together as a single site. This number was part of the inputs.

SampleCoordinates

This is an array which gives the longitude and latitude of each of the found sample sites. The dimension of this array is [SampleSites,2], where the second dimension represents longitude and latitude respectively.

GridCoordinates

An array showing the corresponding coordinates for each longitude and latitude division. The dimension of this array is [2,MaxGridLength], with longitude coordinates coming first and latitude second. Note that one of these rows may not be filled entirely. The associated output GridLength should be used to find the lengths of the two rows. Rows not filled in entirely will contain zeroes at the end.

Author(s)

John Michael Ranola, John Novembre, and Kenneth Lange

References

Ranola J, Novembre J, Lange K (2014) Fast Spatial Ancestry via Flexible Allele Frequency Surfaces. Bioinformatics, in press.

See Also

ConvertPEDData for converting Plink PED files into a format appropriate for analysis,

FitOriGenModel for fitting allele surfaces to the converted data,

PlotAlleleFrequencySurface for a quick way to plot the resulting allele frequency surfaces from FitOriGenModel,;

Examples

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#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

## Not run: 

#Note see the help files for ConvertPEDData and ConvertUnknownPEDData if you have Plink PED files

#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)

#Fitting the model
#MaxGridLength is the maximum number of boxes allowed to span the region in either direction
#RhoParameter is a tuning constant
trials2=FitOriGenModel(TestData,TestCoordinates,MaxGridLength=20,RhoParameter=10)
str(trials2)

#Plotting the model
PlotAlleleFrequencySurface(trials2)


## End(Not run)

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