basic function.txt includes following functions:

  1, mychisq(data) where data is 2 by J contingency table;

  2, rmn(n,size,prob): randomly generate n mulnomial variates;

  3, score(K): generate K*(K+1)/2 by K-1 additive effects score matrix with K-allelic loci;

  4, CATK(data,K): Cochran-Armitage's trend test: for K-allelic loci with score matrix x;

  5, genK.data(n1, n0,alpha,beta=rep(0,K-1),p,K,x=matrix(0,nrow=K*(K+1)/2,ncol=K-1)):   generate data from logistic regression with intercept alpha and scale beta for K-allelic   loci with score matrix x;

  6: CATK2(data,x): Cochran-Armitage trend test for score vector x=(x1,x2,...xj);

  7: genJ.data(n1=n1,n2=n2,n3=n3,n4=n4,alpha,beta,x): generate 2 by 4 contigency table from   logistic regression with intercept alpha, scale beta and with score vector x;



threshold-power-score matrix.txt is a R function (min2) to calculate threshold and power for min2 and pearson's test, Cochran-Armitage trend test with score matrix. The User should specify the following parameters: 

n0: number of controls;
n1: number of cases;
p: allele frequencies of all alleles;
beta1,beta2: genetic effect of risk alleles (beta1=beta2=0 stands for null)
K: number of alleles at the given loci;
x: K*(K+1)/2 by K-1 score matrix;
N.null: number of replicates under null in order to calculate threshold;
N.power: number of replicates to calculate power;




threshold-power-score vector.txt is a R function (general.min2) to calculate threshold and power for min2 and pearson's test, Cochran-Armitage trend test with score vector. The User should specify the parameters same as threshold-power-score matrix.txt does except x is a vector.

permutation.txt includes a R function (pvalues) which returns p-values of min2, pearson's test and Cochran-Armitage test. The user should specify the original data in 2 by J contingency table and the score vector x.