calc.pair.rf.lod {MDSMap}

Create recombination matrix from pairwise data file.

Description

Reads a text file of pairwise recombination fractions and LOD scores and casts it into a matrix of recombination fractions and weights.

Usage

calc.pair.rf.lod(fname, weightfn = "lod", ...)

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.

weightfn

Character string specifiying the values to use for the weight matrix 'lod2' or 'lod'.

...

read.table arguments.

Details

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 with the following elements:

rf

A symmetric matrix of recombination fractions.

nloci

The number of markers in the analysis.

locinames

The names of the markers in the analysis.

Examples

lodrf<-calc.pair.rf.lod(system.file("extdata", "lgV.txt", package="MDSMap"), 
"lod2")