Rmap

NAME

Rmap - Simulate or reformat a map of molecular markers

SYNOPSIS

Rmap [ -o output ] [ -i input ] [ -g gmode ] [ -f mapfunc ] [ -p mapparam ] [ -c chroms ] [ -m MarkersPerChrom ] [ -vm sdMPC ] [ -d InterMarkerDist ] [ -vd sdIMD ] [ -t Tails ] [ -M Mode ]

DESCRIPTION

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.

OPTIONS

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.

-o: 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 qtlcart.map.
-i: 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 ignored.
-g: 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.
-f: 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.
-p: Requires a real number. Some map functions need an extra parameter, and this allows the user to specify it. See the manual for details.
-c: 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.
-m: This allows you to specify the average number of markers per chromosome in a simulation. The default is 16.
-vm: 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.
-d: Rmap uses the value given after this option as the average intermarker distance (in centiMorgans) for a simulation. It is 10 centiMorgans by default.
-vd: 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.
-t: 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 intermarker distances.
-M: 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.

INPUT FORMAT

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).

EXAMPLES

        % Rmap -o Map.out -c 23 -vm 3 -vd 1 -t 5

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
        gnuplot> load "testmap.plt"
        Hit return to continue
        gnuplot> quit

REFERENCES

Genomics

BUGS

Note that if MAPMAKER outputs an intermarker distance of 0.00 cM, then Rmap will translate it to 0.0001 cM. In fact, all intermarker distances of 0.0 will be reset to 0.0001 cM.

Prior to version 1.17d, if you tried to simulate more than 50 linkage groups, you would crash the other programs in the QTL Cartographer Suite. This bug was fixed with version 1.17d.

CONTACT INFO

In general, it is best to contact us via email (basten@statgen.ncsu.edu)

        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
        Phone: (919)515-1934

Please report all bugs via email to qtlcart-bug@statgen.ncsu.edu.

The QTL Cartographer web site ( http://statgen.ncsu.edu/qtlcart ) has links to the manual, man pages, ftp server and supplemental materials.

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