OriGen (version 1.3.1)

FitMultinomialModel: Fit OriGen allele frequency surfaces

Description

This function fits allele frequency surfaces to microsatellite data.

Usage

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

Arguments

DataArray

An array giving the number of alleles grouped by sample sites for each SNP. The dimension of this array is [MaxAlleles,SampleSites,NumberLoci].

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

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

Value

• List with the following components:
• AlleleFrequencySurfaces
  An array giving the allele frequency for each allele, each coordinate, and each SNP. The dimension of this array is [MaxAlleles, NumberLoci, 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 alleles grouped by sample sites for each locus. The dimension of this array is [MaxAlleles,SampleSites,NumberSNPs].
• RhoParameter
  A real value showing the inputted RhoParameter value.
• SampleSites
  This shows the integer number of sample sites 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.
• 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.
• MaxAlleles
  This shows the maximum of AllelesAtLocus. The maximum number of alleles at all loci.
• NumberLoci
  This shows the integer number of loci found.
• 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.
• AllelesAtLocus
  This shows the integer vector of alleles found at each locus.
• 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.

References

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

See Also

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

FitOriGenModel for fitting allele surfaces to the converted SNP data,

FitMultinomialModel for fitting allele surfaces to the converted Microsatellite data,

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

Examples

#Data generation
SampleSites=10
NumberLoci=4
MaxAlleles=4
NumberAllelesAtEachLocus=sample(2:MaxAlleles,NumberLoci,replace=TRUE)

TestData=array(0,dim=c(MaxAlleles,SampleSites,NumberLoci))
for(i in 1:NumberLoci){
	for(j in 1:NumberAllelesAtEachLocus[i]){
		TestData[j,,i]=sample(1:10,SampleSites,replace=TRUE)
	}
}
#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=FitMultinomialModel(TestData,TestCoordinates,MaxGridLength=20,RhoParameter=10)
str(trials2)

#Plotting the model
PlotAlleleFrequencySurface(trials2)