Step 4. Perform Association Testing with ROH Covariates

At this point you can choose to perform association using the fractions provided as they are in the Cluster of Runs spreadsheet (created in Step 3) as covariates or a binarized form of the fractions where any number above ‘0’ is converted to a ‘1’. The latter was done by Dr. Lencz for in his study and the option we will cover in this tutorial.

To binarize the Cluster of Runs spreadsheet you need to download the Convert to Binary our Add-on Script Repository

Save this script to the following directory: ../HelixTree/scriptsHT/user/Spreadsheet/Edit/.

Next, from the Cluster of Runs spreadsheet select >Edit >Convert to Binary. The following dialog will appear:

The idea here is to input a threshold value above zero that is lower than the smallest fraction in the Cluster of Runs spreadsheet. Since the smallest possible fraction in this case is 1/100, inputting .001 will be sufficient to convert all nonzero numbers to ‘1’. Enter the number and click OK.

The result will be a new spreadsheet with ‘1s’ and ‘0s’ (Figure 2).

Next you need to join this spreadsheet with the phenotype spreadsheet imported in Step 1.

Open the phenotype spreadsheet and select >File >Join Spreadsheets on Row Labels. A Spreadsheet Chooser window will appear (Figure 3) prompting you to select a spreadsheet to join with.

Select the Binary Values Data Set – Sheet 1 and click OK. A new spreadsheet will be created containing both case/control status and the binary ROH covariates.

You can now perform association using interactive tree analysis and the regression module. To perform interactive tree analysis Left Click the Case/Control column header to turn the column magenta (Figure 4) and select >Analysis >Interactive Tree Analysis. To perform regression (logistic in this case) select >Analysis >Regression Analysis.

Performing association and interpreting association results is not covered in this tutorial, but such functionality is discussed at length in the Interactive Tree Analysis and Regression Analysis chapters of the HelixTree Manual.