Rmap creates a random map of molecular markers. The user specifies the number of
chromosomes, the number of markers per chromosome and the average intermarker
distance. If one specifies standard deviations for the number of markers and the
average intermarker distances, they will vary subject to the normal
distribution. The output gives a table of markers by chromosomes, with the
distances between consecutive markers (in centiMorgans) in the table.
If you specify an input file, Rmap will open it, determine if it is in
the same format as Rmap outputs, and process it based in the value
given to -g. If the input file is the output of MAPMAKER, then the
map will be reformatted from MAPMAKER into the Rmap output format.
Finally, there is a standard input format that Rmap can translate, and
is defined in the file map.inp that comes with the distribution of the
programs. Note that if the user specifies an input file, no simulations
will be done and the latter half of the command line options are ignored.
See QTLcart(1) for more information on the global options
-h for help, -A for automatic, -V for non-Verbose
-W path for a working directory, -R file to specify a resource
file, -e to specify the log file, -s to specify a seed for the
random number generator and -X stem to specify a filename stem.
The options below are specific to this program.
If you use this program without specifying any options, then you will
get into a menu that allows you to set them interactively.
This should be used with a filename indicating where the output will be
written. Rmap will overwrite the file if
it exists, and create a new file if it does not. If not used, then Rmap will use
You can use this option to specify an input filename. This file must exist and have
one of three formats: Rmap.out, map.inp or mapmaker.mps. Rmap will
attempt to identify the format of the file and translate it to another format.
If you specify an input file, then the simulation parameters will be
Requires an integer to indicate the output format. You can use
a 1 for the default ouput format, a 2 for GNUPLOT output or
a 3 for both. If you use a 2 or a 3, then you can use GNUPLOT
to see graphical version of the linkage map.
Requires an integer option to specify the mapping function.
Rmap can use the Haldane, Kosambi, fixed or a number of other functions.
The default is to use the Haldane function, which is specified with a 1.
Using a 2 invokes the Kosambi mapping function. A 3 means that a fixed function is used
and thus the distance in Morgans is the recombination fraction. The type
of mapping function used would then be recorded in the ouput and all following analyses will
use this function. One must edit the map file to change this if not using Rmap.
This allows you to specify the number of chromosomes if you are simulating a
genetic linkage map. It is 4 by default. If you are translating a
file, then this will be ignored as will the remaining options.
This allows you to specify the standard deviation in the number of markers per chromosome.
The number of markers per chromosome will have a normal distribution with
mean given in the previous option, and the standard deviation specified here. If zero,
then each chromosome will have the same number of markers.
The intermarker distance will have a normal distribution with mean
set by the previous option and standard deviation specified with this
option. It is 0.0 by default, which means that the intermarker distances
between consecutive markers will all be the same. Set it to a positive value to
have intermarker distances vary at random.
You can simulate maps where there are no markers on the telomeres with this option.
Give this option a value of tails and Rmap puts an average of tails
Morgans of genetic material on the ends of the chromosomes. By default, it
is 0.0. If the standard deviation for intermarker distance is greater than 0.0, then
then the amount of flanking DNA will have a normal distribution with mean given here
and standard deviation proportional to that of the standard deviation of
Allows you to specify an alternate simulation mode. If the -M
option is used with a value of 1, then the intermarker distance will be used
as the chromosome length (so you should make it longer), and the markers are
placed on the chromosomes following the uniform distribution.
The value of this option will be returned to 0 at the completion of the program.
Rmap recognizes four types of files. The first is the Rmap.out format
that Rmap itself creates. The second is a special format defined in the example
file map.inp included in the distribution. The third format is the
output of MAPMAKER. If the input file is a MAPMAKER output file,
Rmap translates this file into its own format. If the input file is already in the
correct format, Rmap will output it dependant upon the flag given to
the -g option. The units of intermarker distances will be in
centiMorgans in the output.
Rmap also recognizes the input files for the Windows GUI version of QTL Cartographer
(Wang, et al., 2002).
Simulates a random map where the number of markers on each of 23 chromosomes has
a normal distribution with mean 16 and standard deviation 3. The intermaker distance is
normally distributed with mean 10 cM and standard deviation 1. There will be some
genetic material outside the flanking markers on each chromosome, with a
mean length of 5 cM and standard deviation 0.5.
% Rmap -o Map.out -i map.mps
Opens the file map.mps, tries to determine its format, and translates it if
possible. The output will be written to the file Map.out. The extension .mps
should be used with MAPMAKER output files and the string -filetype mapmaker.mps
should be put somewhere in the first twenty lines of the file.
% Rmap -i map.inp -g 3 -X test
This opens the file map.inp and translates it. Two output files are produced.
The file test.map contains the genetic linkage map in Rmap.out format, while
a file testmap.plt contains code for GNUPLOT. The next step would be to
start GNUPLOT and load testmap.plt.
gnuplot> load "testmap.plt"
Hit return to continue
Lander, E. S., P. Green, J. Abrahamson, A. Barlow, M. Daley, S. Lincoln and
L. Newburg (1987) MAPMAKER: An interactive computer package for constructing primary
genetic linkage maps of experimental and natural populations.
Wang, S., C. J. Basten and Z.-B. Zeng (2002) Windows QTL Cartographer: WinQtlCart V2.0.
T. Williams and C. Kelley (1993) GNUPLOT: An Interactive Plotting Program. Version 3.5
Christopher J. Basten, B. S. Weir and Z.-B. Zeng
Bioinformatics Research Center, North Carolina State University
1523 Partners II Building/840 Main Campus Drive
Raleigh, NC 27695-7566 USA