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.
sim.bc.rflod.file(fname)a character string specifying the base name of the file fname.txt to which the data should be written
No output - just the text file as above
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.
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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