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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.
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BMC Genomics

ISSN: 1471-2164

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