13.3 Running lm_map with genotypic data

Run the genotypic example in the `Map' subdirectory of the `MORGAN-examples' directory with the following command

./lm_map map_G.par

The lm_map program is one of the more computationally intensive MORGAN programs. Even running this small example takes about 30 seconds to run (depending on the computer used, of course). Again, different random seeds will result in different outputs with each run.

Here is the output from one of the runs: The maximum likelihood estimates (MLEs) of marker map recombination frequencies are given for each marker interval and for male and female meioses. Also given is the estimated variance-covariance matrix of the MLEs. Of course, the MLE will not be identical to the true parameter value, but the variance-covariance matrix gives an estimate of the precision. The `effective number of meioses' is also a measure of this precision, giving the number of fully informative meioses required for the same precision of the MLEs.

MAXIMUM LIKELIHOOD ESTIMATES Interval Female (RF) Male (RF) -------- ----------- --------- 1 0.2231 0.0264 2 0.2745 0.0801 ESTIMATED VARIANCE OF SEX-SPECIFIC MAP [F1,M1,F2,M2,... x F1,M1,F2,M2,...] 0.004402 -0.000034 -0.000422 -0.000040 -0.000034 0.000621 0.000075 -0.000025 -0.000422 0.000075 0.006546 -0.000136 -0.000040 -0.000025 -0.000136 0.001482 EFFECTIVE NUMBER OF MEIOSES Interval Female Male -------- -------- ------- 1: 40 42 2: 31 50