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