Step 3. Run PBAT CNV Analysis

Now that you have a DSF file created and the pedigree spreadsheet loaded into your project, you can perform PBAT copy number analysis. To do this, from the main project window go to >PBAT >PBAT CNV Analysis. The window in Figure 1 will open.

It looks similar to the window for PBAT SNP analysis with a few extra inputs at the top.

From this window first Browse to the 30_common_final.dsf file downloaded in Step 1. Once you select the file, the Chromosomes box will fill in with all 23 chromosomes (Figure 2). You can choose to analyze all chromosomes simultaneously or select a subset by clicking the Choose button at the right.

For the purpose of this tutorial, select only chromosome ‘22’. To do this click the Choose button, then click Uncheck All, and select ‘22’. Click OK. (Resulting window not shown.)

Next, Browse to the 30_common_ped pedigree spreadsheet imported during Step 2 (Figure 3).

Next, you need to indicate how the LogRs and pedigree information will be matched up. In this case, because both the LogR DSF file and the pedigree spreadsheet have matching row labels you can select the middle button DSF and spreadsheet label (Figure 4).

If you imported an FBAT Pedigree into your project, choose the DSF labels with spreadsheet column option. A list of column headers in your pedigree spreadsheet will appear. Select the column that matches the row label column in your LogR DSF file. In most cases, this will be the Patient ID column.

If you do not have a column in your pedigree spreadsheet matching the Sample names in your DSF file, you can use the Default DSF and spreadsheet order option. This option is not recommended as it will only work if your DSF file rows are in the exact order as your pedigree spreadsheet rows.

After these first four parameters are set, the rest of the process is similar to that of PBAT SNP analysis. You can choose the affection status or select a Phenotype Spreadsheet and then go through each tab and set the parameters accordingly. When you are finished setting all the parameters click Run Analysis.

When the analysis is finished the following window will appear indicating 6,206 rows were imported. This corresponds to the number of LogRs analyzed (chromosome 22 has 6,206 markers on the 500k CEL file.

Click OK. The following results spreadsheet will be loaded into the project.

Notice, the only two columns having differing results are the pvalue (FBAT) and pvalue (Wald). This is because power calculations are not currently supported for PBAT CNV analysis.

From here you can sort each p-value column by left clicking on the column number (e.g. 2 or 6) and selecting Plot this column. You will get a p-value plot similar to the one below.