calc.nnfit.from.file {MDSMap}

Nearest neighbour fit from estimated map and file of pairwise recombination fractions.

Description

Calculates a nearest neighbour fit based from an estimated map and a file containing pairwise recombination fractions and LOD scores.

Usage

calc.nnfit.from.file(estmap, fname, mapfn = "haldane", n = NULL,
  header = FALSE)

Arguments

estmap

A character string indicating the name of a comma separated value file with the first column containing marker names in the order of their estimated position.

fname

A 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.

mapfn

Character string, 'haldane', 'kosambi' or 'none' specifying the values to use to estimate the map distance from the recombination fractions. Default is 'haldane'.

n

Vector of character strings or numbers specifying the markers to be omitted from the analysis. Default is NULL.

header

Logical argument indicating whether the .csv file estmap contains headers - default is TRUE

Details

Reads in two files fname.txt and estmap.

The data is cast the data into symmetric matrices of pairwise recombination fractions and LOD scores with the order of columns and rows in the matrix determined by the order specified in estmap. A distance matrix is calculated according to the method specified by mapfn. Haldane is the default map function, None just uses recombination fractions and the other alternative is Kosambi (see dmap for details). The nearest neighbour fit is then calculated (see calc.nnfit for details)

estmap should contain marker names in the first column in the order of the estimated map.

fname 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:

fit

Sum over all markers of the nearest neighbour fits.

pointfits

The nearest neighbour fit for each marker.

meanfit

Mean of the nearest neighbour fits over all markers.

See Also

dmap, calc.nnfit, calc.pair.rf.lod