CE: Cross entropy Monte Carlo methods for SNP selection

This MATLAB toolbox is for  SNP selection  (tagging) from haplotypes with thousands SNPS.  The 
idea is to maximize the generalized entropy ratio (ER) related criteria with cross entropy monte carlo 
method.

Requirements:

* A MATLAB environment. 

  * Octave is not supported.


Install:

  simply add a directory where you have unpacked *.m into MATLAB path. For
    example:
    % cd ~/work
    % tar xvfz CE.tar.gz 
    % cd CE/
    % matlab
    >> addpath ~/work/CE


Download:

CEMC.tar.gz

performance:

The matlab version requires serveral  hours for over 1,000 SNPs and hundreds of  distinct haplotypes. C version should be much 
faster since it can deal with  strings more efficiently. There in NO C version available currently. I might write a C version 
 in the near future.

Format:

Haplotype   Frequency.
 1 1 1 1 2         0.2
...... 


Functions:

[finalp, curbests, Zg, ps, gammas] = hapcemc2(haplist, shap, Fhap, N, rho, maxIters, epn, lamda, pr)

This is the main funtion for CEMC.
Input:
haplist: haplotype list
Shap: the string version of haplotype  (We have to use strings for haplotype for large data set)
Fhap:  the haplotype frequency
N:       sample size 
rho:     The proportion in important sampling
MaxIters: the maximum iterations
epn:   stop criteria
lamda: is the weight
pr:       initial probability

output:

finalp: the final probability each SNP is choosen
curbest: best result for each iteration:


demos:

%load hap51;
 
% S = strread(X);
% for lam = 0.3:0.1:0.7.
    
%    [fp, bst] =hapcemc2(X, S, F,  1000, 0.15, 100, 0.00001, lam);
% end

% c = find(fp > 0.5);
% H=11;
%vb = perform(X, F, c,  H, 0)

Reference:

1. Liu, Z., and  Lin, S. 2005 Multilocus LD measure and tagging SNP selection with generalized mutual
     information. Genet Epidemiol. 29, 353-364.

2. Liu, Z., Lin, S., Tan, M. (2006) Genome-wide tagging SNPs with entropy-based Monte Carlo methods. 
Journal of Computational Biology, accepted

3. Weale, M.E., Depondt, C., Macdonald, S.J., Smith, A., Lai, P.S.,
Shorvon, S.D., Wood, N.W., and Goldstein, D.B. 2003.
Selection and evaluation of tagging SNPs in the neuronal-sodium-channel gene SCN1A:
 implications for linkage-disequilibrium gene mapping.
Am J Hum Genet 73, 551-565. (The perform.m and performl.m functions are revised from Weale's TAGIT3.0 package)