As an exercise in learning to use the programs, you can simulate a genetic linkage map. The main parameters that you will need to specify are the haploid number of chromosomes, average number of markers per chromosome, and average intermarker distance between consecutive markers. You can also simulate linkage maps in which the telomeres don't have marker information.
Figure 2.3 shows how Rmap simulates a genetic linkage map where is marker on chromosome . We denote the number of chromosomes by , the average number of markers per chromosome by and the average intermarker distance by in centimorgans. Furthermore, the average amount of ``tail'' DNA (DNA outside the most telomeric markers) will be specified by , again in centimorgans. The standard deviations of and will by and , respectively. All of these variables can be specified by command line options, the resource file or by the interactive menu. The standard deviation of will be . For the th chromosome, Rmap decides how many markers are on that chromosome by picking a random number from a normal distribution with mean and standard deviation . Once this is done, the amount of DNA between consecutive markers is simulated as a normal random variable with mean and standard deviation . Finally, the amount of telomeric or tail DNA is simulated as a normal random variable with mean and standard deviation . Setting a standard deviation equal to zero means that the quantity in question is not a random variable, but set equal to its mean value.
The parameters and can be set using the command line options of Table 2.1 or in the interactive menu. Note that if an input file is specified, all these parameters are ignored and Rmap attempts to translate the input file.
An alternate method of simulating the genetic linkage map can be invoked by changing the simulation mode parameter from 0 to 1 using the -M command line option. Figure 2.4 presents the method graphically. The length of chromosome () will be normally distributed with mean and standard deviation . The number of markers on chromosome () will still be normally distributed with mean and standard deviation , but will be placed on the chromosome following a uniform distribution on the interval . You should set the values of and to appropriate levels, as they are for chromosome length rather than intermarker distance in this mode. For example, if you want roughly the same results from this mode as that in the original, then set in this mode.