Haploview provides a framework for permuting your association results in order to obtain a measure of significance corrected for multiple testing bias. You can choose to permute one of several test sets:
Single Markers Only
Permute just association tests to the individual SNPs in your dataset.
Single Markers and Haplotypes in Blocks
Permute the individual SNPs as above, along with all the haplotypes shown in the Haplotypes tab.
Haplotypes in blocks only
Permute only the haplotypes in the Haplotypes tab, ignoring the single marker results.
- Custom Tests from File
Permute the set of tests loaded from an external file. Note that this choice is only available if you provided a tests file when you loaded your dataset.
- A progress bar which tracks the progress of the permutations.
- The highest permuted chi square so far.
- The fraction of permutations whose strongest association exceeds the best observed chi square.
- A table listing all tests (single SNP and haplotype) along with their association chi squares and permuted p-values.
- A histogram of the highest chi square from each of the permutations.
Specify how many permutations to do and press the "Do Permutations" button to start the permutations. While the permutations are running, Haploview shows the following:
You can stop the permutations at any time with the "Stop" button.
You can save the permutation summary by using the "Export Tab to Text" option in the File menu.