4 Joint Effects

For full details of the joints effects test and the accompanying notation please refer to the manuscript by Ueki and Cordell (2012).

4.1 Options

The options that are specific to the joint effects test are:

Option	Description
-thcc t	P-value threshold for case/control test (set to 0 for no output)
-thco t	P-value threshold for case only test (set to 0 for no output)
-th t	P-value threshold for either test (set to 0 for no output)

CASSI performs both the case-only test and case-control test for each pair of tested SNPs. 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 -th option. The default value for both thresholds is 0.0001.

For other basic options see section 3.1.

4.2 Input Files

The input files should be given in the binary PLINK format as explained in section 3.

4.3 Output Files

The output file from running a joint effects SNP interaction analysis using CASSI will look something like the following:

SNP1 SNP1_Name SNP2 SNP2_Name Case_logOR Case_SE Con_logOR Con_logSE
 Case-Con_Chisq Case-Con_Pval Case-Only_Chisq Case-Only_Pval
4 rs123456 56 rs2345 4.13044 0.946829 3.96474 0.983261 0.00910349 0.923987 15.2945 9.1984e-05
4 rs123456 73 rs2365 4.19374 1.09557 5.31239 1.01136 0.0720141 0.788426 21.1098 4.33708e-06
4 rs123456 74 rs342345 3.93546 1.02951 5.40301 0.878292 5.89417e-06 0.998063 16.4154 5.08706e-05
...

The first line is a header labelling the columns of the results file. The SNP number and SNP names 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.

Case_logOR is the log odds for the cases and is given by $\tilde{\lambda}_A$ . If the alternative test is used this is given by $\tilde{\mu}_A$ .

Case_SE is the standard error for $\tilde{\lambda}_A$ and is given by $\tilde{\nu}_A$ . If the alternative test is used the standard error for $\tilde{\mu}_A$ is recorded, given by $\tilde{\nu}_{\mu_A}$ .

Con_logOR is the log odds for the controls and is given by $\tilde{\lambda}_N$ . If the alternative test is used this is given by $\tilde{\mu}_N$ .

Con_SE is the standard error of the controls test and is given by $\tilde{\nu}_N$ . If the alternative test is used the standard error for $\tilde{\mu}_N$ is recorded, given by $\tilde{\nu}_{\mu_N}$ .

Case-Con_Chisq is the $\chi^2$ test statistic with one degree of freedom for the case-control test.

Case-Con_Pval is the corresponding p-value for the case-control test.

Case-Only_Chisq is the $\chi^2$ test statistic with one degree of freedom for the case-only test.

Case-Only_Pval is the corresponding p-value for the case-only test.

<-prev