Class MaxTwoPointLods
java.lang.Object
MaxTwoPointLods
public class MaxTwoPointLods
- extends java.lang.Object
This program finds the maximum lod score for values of the
recombination between 0 and 1 (not 0 and 0.5).
Usage : java MaxTwoPointLods input.par input.ped
where
- input.par is a LINKAGE parameter file
- input.ped is a LINKAGE pedigree file
The results are written to the standard output file as a bare table
with a row for each marker and two columns. The first column gives
the maximizing value of the recombination fraction and the second
gives the maximized lod score.
The method used is a golden section search that takes about 20
function evaluations to get to within 0.001 of the maximizing value.
The program maximizes the lod scores separately over the two intervals
(0,0.5) and (0.5,1), because there may be a local maximum in each
of these intervals. The output is a bare table of 4 columns
giving the maximizing value and maximum in the region (0,0.5)
followed by the maximizing value and maximum in the region (0.5,1).
Values of the recombination paramter in the region (0.5,1) have
no genetic interpretation, but may occur if the phase information
is low and/or the model is misspecified.
If you don't think you want values in the (0.5,1) region, just
ignore the last two columns.
|
Method Summary |
static void |
main(java.lang.String[] args)
|
| Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
MaxTwoPointLods
public MaxTwoPointLods()
main
public static void main(java.lang.String[] args)