Originally, the program Rmap was designed to simulate a genetic linkage map. The ``R'' in Rmap was meant to convey the meaning of ``Random Map''. Since then we have included the ability to translate genetic linkage map information from various formats into that required by the QTL Cartographer system. Thus, the ``R'' can now mean reformat or random.
If you have no data, you can simulate a genetic linkage map. Rmap allows the user to specify the number of chromosomes, markers per chromosome and average intermarker distance for the simulation. You can also specify standard deviations for the latter two quantities. This would yield a simulated map that better approximates one that you might actually produce in the lab. Finally, you can also specify whether you want some genetic material outside the most telomeric markers on the chromosomes.
Rmap can also read in files in three formats. The first format is the same as its output format. We will refer to this as ``Rmap.out'' filetype format. This feature is provided so that you can create as set of output files that Gnuplot can read and display a graphic representation of your markers.
The second format is that which is produced by Mapmaker/EXP landeretal@87,lincolnetal@92b: We will refer to it as a ``mapmaker.maps'' filetype format. Rmap will read in the Mapmaker/EXP output and reformat into the ``Rmap.out'' format. The third format is defined in Section 6.1.2 and in the file map.inp included with the distribution of the programs. Remember: Rmap will overwrite output files. If you specify an output file that already exists, Rmap will destroy it when creating a new file. For this reason, we recommend that all work is done in a working subdirectory on copies of the original input files.