== TEAM == 

[How to compile]
  0) This program is running in Windows system. The following development environment is needed:
     Visual Studio V8.0, Boost 1.35
     For how to install and configure Boost, please refer to http://www.boost.org/doc/libs/1_35_0/more/getting_started/windows.html.

  1) Import both projects into Visual Studio
  2) then compile the program

[Usage] 
  .\TEAM-win -if_geno geno_fn -if_pheno pheno_fn -n_inds #individuals -n_snps #SNPs -n_perms #permutations -of_pvalue pvalue_file
  .\get_snps -if_geno geno_fn -if_pheno pheno_fn -n_inds #individuals -n_snps #SNPs -n_perms #permutations -if_qvalue pvalue_file -qvalue threshold 

  
[Options Details]
geno_fn: 	the genotype data file name (the rows are SNPs, the columns are individuals)
pheno_fn: 	the phenotype data file name
pvalue_fn:  the pvalue output file name
#individual: 	the number of individuals in the data
#SNPs: 		the number of SNPs in the data
#permutations:	the number of permutations used in the significant test
#qvalue_threshold:the FDR threshold for significance

[Example]
  .\TEAM-win -if_geno ..\data\genotypes_1k_2520.txt -if_pheno ..\data\phenotypes_2520.txt -n_inds 2520 -n_snps 1000 -n_perms 100 -of_pvalue tmp.txt
  .\get_snps -if_geno ..\data\genotypes_1k_2520.txt -if_pheno ..\data\phenotypes_2520.txt -n_inds 2520 -n_snps 1000 -n_perms 100 -if_qvalue tmp.txt -qvalue 0.2

[Output Description]

  ======Significant SNP-pairs=====     <---- List of Significant SNP-pairs
  SNP-pair (284,70):42.5534            <---- SNP-pair (Xi,Xj): Test score
  SNP-pair (284,76):38.5984
  SNP-pair (284,74):41.0445
  SNP-pair (283,70):38.6654
  ================

Ver 0.0.4_win32
@All Rights Reserved.
