Table 2

HFCC analysis: Preliminary results and effect of noise filters.

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%


Method I: Only Direction Filter applied.

Method II: Direction and Tracking filters applied.

Method III: All filters applied (Control, Direction, and Tracking filters sequentially in that order).

N: Number of selected two-locus SNP pairs.

%: Percentage of selected two-locus SNP pairs over the preliminary set (unfiltered HFCC results).

A total of 36 SNPs were identified as tracking SNPs in the two methods using tracking filter.

Gayán et al. BMC Genomics 2008 9:360   doi:10.1186/1471-2164-9-360

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