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Table 2 HFCC analysis: Preliminary results and effect of noise filters.

From: A method for detecting epistasis in genome-wide studies using case-control multi-locus association analysis

Applied Filters Unfiltered Results After Control Filter After Direction Filter After Tracking Filter Selected two-locus SNP pairs
      Simultaneous Conditional Epistatic
Method I        
   N 418,535 - 320,265 - 71,332 248,898 35
   % 100% - 76.5% - 17.0% 59.5% 0.01%
Method II        
   N 418,535 - 320,265 26,371 19,630 6,706 35
   % 100.0% - 76.5% 6.3% 6.1% 2.1% 0.01%
Method III        
   N 418,535 340,043 320,188 26,347 19,611 6,701 35
   % 100.0% 81.2% 76.5% 6.3% 6.1% 2.1% 0.01%
  1. Method I: Only Direction Filter applied.
  2. Method II: Direction and Tracking filters applied.
  3. Method III: All filters applied (Control, Direction, and Tracking filters sequentially in that order).
  4. N: Number of selected two-locus SNP pairs.
  5. %: Percentage of selected two-locus SNP pairs over the preliminary set (unfiltered HFCC results).
  6. A total of 36 SNPs were identified as tracking SNPs in the two methods using tracking filter.