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 a primitive looking 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.