# 6 Adjusted Fast Epistasis

The adjusted fast epistasis test is a corrected version of the fast epistasis test as implemented in PLINK Purcell et al. (2007), and is described by Ueki and Cordell (2012). Despite requiring some extra calculation the adjusted fast epistasis test in CASSI runs faster than the fast epistasis test in PLINK, see section 10.3 for details.

The options that are specific to the adjusted fast epistasis test are:

Option | Description |

-afe | perform the adjusted fast epistasis test |

-afe-thcc t | p-value threshold for case/control test |

-afe-thco t | p-value threshold for case only test |

-afe-th t | p-value threshold for either test |

-afe-cc-only | perform the case/control test only |

-afe-co-only | perform the case only test only |

-afe-so | suppress results of test |

CASSI performs both the case only test and case/control test for each pair of tested SNPs by default. SNPs that are too close for the case only test, as definded by the `-gap` option, are not tested. The results of the test are recorded for the pair of SNPs if *either* p-value threshold is met. Both thresholds may be set simultaneously by using the `-afe-th` option. The default value for both thresholds is 0.0001.

For other basic options see section 3.2.

The output file from running an adjusted fast epistasis SNP interaction analysis using CASSI will look something like the following:

SNP1 CHR1 ID1 BP1 SNP2 CHR2 ID2 BP2 AFE_CASE_LOG_OR AFE_CASE_SE AFE_CTRL_LOG_OR AFE_CTRL_SE AFE_CC_CHISQ AFE_CC_P AFE_CO_CHISQ AFE_CO_P
2 1 rs1103289 207421 5 1 rs1233280 221980 6.15411 1.08027 5.9423 1.0608 0.0195714 0.888741 32.454 1.22046e-08
2 1 rs1103289 207421 6 1 rs498039 222598 6.7911 1.18655 6.7911 1.18655 0 1 32.7571 1.04422e-08
2 1 rs1103289 207421 12 1 rs65417 242851 4.28441 1.00451 4.80692 1.01244 0.134221 0.714096 18.1915 1.99764e-05
2 1 rs1103289 207421 25 1 rs1246136 361265 6.7911 1.18655 6.7911 1.18655 0 1 32.7571 1.04422e-08
2 1 rs1103289 207421 46 1 rs1246300 739776 6.7911 1.18655 6.7911 1.18655 0 1 32.7571 1.04422e-08
...

The first line is a header labelling the columns of the results file. The SNP details for the pair of SNPs are given firstly followed by values calculated from the joint effects tests. Results are given for both the case only test and for the case/control test regardless of which p-value was significant enough to record the pair of SNPs. The case only test assumes that the two SNPs are in linkage equilibrium in the general population, so care must be taken in interpreting results with SNPs that are near one another. See Ueki and Cordell (2012).

**AFE_CASE_LOG_OR** is the log odds ratio for association in the cases.

**AFE_CASE_SE** the standard error of AFE_CASE_LOG_OR.

**AFE_CTRL_LOG_OR** is the log odds ratio for association in the controls.

**AFE_CTRL_SE** is the standard error of AFE_CTRL_LOG_OR.

**AFE_CC_CHISQ** is the test statistic with one degree of freedom for the case/control test.

**AFE_CC_P** is the corresponding p-value for the case/control test.

**AFE_CO_CHISQ** is the test statistic with one degree of freedom for the case only test.

**AFE_CO_P** is the corresponding p-value for the case only test.