== FastANOVA == 

[How to compile]
  0) This program is running in Linux system. The following packages may be required:
     boost-1.35, cmake, g++-4
  1) Get into the FastANOVA directory, and run "cmake .".
  2) then run "make"

[Usage] 
  ./fastanova geno_fn pheno_fn #individuals #SNPs #permutations FWER_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
#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
#FWER_threahold:the threshold of Family-wise Error Rate Control

[Example]
  ./fastanova ../data/genotype_file.txt ../data/phenotype_file.txt 32 1000 100 0.1

[Output Description]
  #=== Step 1: Finding Critical Value in Permutations ===#            
  #Critical Value(F_alpha):                                          <---- the threshold use to prune
  21.0228

  #------------ Step 1 Runtime Statistics ----------#
  #Run time: 19.45  seconds
  #Visited pairs: 12120898
  Pruning raio:0.757339
  #------- End of Step 1 Runtime Statistics --------#


  #======= Step 2: Finding Significant SNP pairs ========#
  #Num of Significant SNP pairs                                      <---- the number of significant SNP-pairs found
  1
  #-------------- Significant SNP pairs ------------#                <---- the list of significant SNP-pairs
  #F Value: 
  25.4018
  #Genotype Id: 
  334                                                               
  00000000000011001110000111011101
  #Genotype Id: 
  625
  11000000001000000001111000100010
  #------------------------------#

  #---------- End of Significant SNP pairs ---------#

  #------------ Step 2 Runtime Statistics ----------#
  #Run time: 0.46  seconds
  #------- End of Step 2 Runtime Statistics --------#

  @@100
  Running time: 19.91  seconds



Ver 0.0.5
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