Simulating a Map

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.