Output Flags

The output flag takes on values of 1, 2 or 3. A 1 indicates that Rmap should output a file in the ``Rmap.out'' format. A 2 indicates that a set of files that can be plotted in Gnuplot should be created while a 3 indicates that both should be done. The option to display the map in Gnuplot allows a general overview of the spacing of markers. If you choose to create the Gnuplot files, then Rmap will write one file per chromosome summarizing the linkage information. Each file will have two columns: The first indicating the position of the marker from the telomere and the second for the chromosome number. The file for chromosome 1 will be Chrom.1, and other files are named accordingly. Finally, a control file, Chrom.plt, will have the plotting commands understood by Gnuplot. This file should be loaded by Gnuplot to view the linkage map. Marker names are not written on the map.