calc.maps.sphere {MDSMap}

Estimate marker positions using spherically constrained weighted MDS

Description

Reads a text file of pairwise recombination fractions and LOD scores, estimates marker positions using spherically constrained weighted MDS

Usage

calc.maps.sphere(fname, p = 100, n = NULL, weightfn = "lod2",
  mapfn = "haldane")

Arguments

fname

Character string specifying the base name of the file fname.txt which contains the data to be analysed. The file should be white space or tab separated.

p

Integer - the penalty for deviations from the sphere - higher p forces points more closely onto a sphere.

n

Vector of integers or strings containing markers to be omitted from the analysis.

weightfn

Character string specifying the values to use for the weight matrix in the MDS 'lod2' or 'lod'.

mapfn

Character string specifying the map function to use on the recombination fractions 'haldane' is default, 'kosambi' or 'none'.

Details

This can be very slow with large sets of markers, in which case it may be better to consider calc.maps.pc.

Reads a file of the form described below and casts the data into matrices of pairwise recombination fractions and weights determined by the weightfn parameter (LOD or LOD^2^) calculates a distance matrix from the map function. Haldane is the default map function, None just uses recombination fractions and the other alternative is Kosambi (see link{dmap} for details).

Performs both an unconstrained and dual spherically constrained weighted MDS on the distance matrix using smacofSym and smacofSphere (de Leeuw & Mair 2009) and maps this to an interval (see map.to.interval for details).

Inevitably the constrained MDS has higher stress than the unconstrained MDS and a good rule of thumb is that this should not be more than about 10

File names should be of the form fname.txt and it is assumed that they are in a tab or space separated file of the format displayed below. The first entry on the first row is the number of markers to be analysed. Underneath this is a table in which the first two columns contain marker names, the third column contains the pairwise recombination fractions between the markers and the fourth column the associated LOD score. Note that marker names in the first column vary more slowly than in the second column. Missing recombination pairs are acceptable. Recombination fractions greater than 0.499999 are set to that value.

nmarkers
marker_1	marker_2	recombination fraction	LOD
1	2	.	.
1	3	.	.
1	4	.	.
.	.	.	.
.	.	.	.
.	.	.	.
2	3	.	.
2	4	.	.
.	.	.	.

Value

A list (S3 class 'spheremap') with the following elements:

smacofsym

The unconstrained wMDS results.

smacofsphere

The spherically constrained wMDS results.

mapsphere

Map of the markers onto an interval containing order-the rank of each marker.

distmap

A symmetric matrix of pairwise distances between markers where the columns are in the estimated order.

lodmap

A symmetric matrix of lod scores associated with the distances in distmap.

locimap

A data frame of the markers containing the name of each marker, the number in the configuration plot if that is being used, the position of each marker in order of increasing distance and the nearest neighbour fit of the marker.

length

Integer giving the total length of the segment.

removed

A vector of the names of markers removed from the analysis.

locikey

A data frame showing the number associated with each marker name for interpreting the wMDS configuration plots.

stressratio

The ratio of the constrained to unconstrained stress.

ssphere

The stress per point of the spherically constrained wMDS.

ssym

Stress per point of the unconstrained wMDS.

meannnfit

The mean across all markers of the nearest neighbour fits.

References

de Leeuw J, Mair P (2009) Multidimensional scaling using majorization: SMACOF in R. J Stat Softw 31: 1-30 http://www.jstatsoft.org/v31/i03/

See Also

calc.maps.pc, calc.pair.rf.lod, smacofSym, smacofSphere, map.to.interval, dmap, calc.nnfit

Examples

smap<-calc.maps.sphere(system.file("extdata", "lgI.txt", package="MDSMap"),
weightfn='lod',mapfn='kosambi')