This directory contains programs to accompany

Dmitri V. Zaykin, Zhaoling Meng, Margaret G. Ehm. 2006. Contrasting LD
patterns between cases and controls as a novel association mapping
method. AJHG, in press.

testdat.txt: A simulated data set; phenotype is the column 1, plus 5 SNPs

First, SNPs in a file like this need to be re-coded to -1,0,1
(11 -> -1;  12 -> 0;  22 -> 1). This can be done with the perl
script in this directory:

   recode_to_-1_0_1.pl x testdat.txt > testdat-recoded.txt

'x' is a missing data label; testdat-recoded.txt is the output

Please see "sample.Rhistory.txt" on the usage of R scripts for matrix
LD comparisons.

The programs are currently being improved - please let me know if you
plan to use them.

Dmitri