sim.bc.rflod.file {MDSMap}

Simulate a backcross population from homozygous parents.

Description

Simulates a backcross population from homozygous parents and writes a file containing the number of markers and observed pairwise distances, the pairwise recombination fractions and LOD scores in a text file suitable for analysis by other functions in the package.

Usage

sim.bc.rflod.file(fname)

Arguments

fname

a character string specifying the base name of the file fname.txt to which the data should be written

Details

This function simply generates data for use with the vignette. The R/qtl package is used to simulate a backcross #'population of 200 individuals from homozygous parents with 200 markers in a single linkage group of length #'100cM. The recombination fractions and LOD scores are calculated. The data is written to a text file in the #'format of output from JoinMap 4. In particular, the data is cast into a data frame with marker names in the #'first two columns, pairwise recombination fractions in the third column and associated LOD scores in the fourth #'column. The data is written to a text file 'fname.txt' where the first row contains two entries - the number of #'markers and the number of pairwise observations. Below this the data frame containing the distance data is #'appended with no column headings.

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

Value

No output - just the text file as above

References

Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics. 189: 889-890 Van Ooijen JW (2006) JoinMap 4; Software for the calculation of genetic linkage maps in experimental populations. Wageningen; Netherlands: Kyazma B.V