In addition to the annotation based on available data from public databases, many other interesting and important questions could be raised. For example, what are the Hardy-Weinberg Equilibrium (HWE) results for the top hits? What are the effect sizes, effect directions, etc, for these SNPs of most interest?
WGAViewer offers a convenient interface to allow the user to load many kinds of customized supporting/QC data to list alongside the SNP lists of interest, in addition to the annotation from public databases. We illustrate this function using our pre-annotation example set “CHAVI_SETPOINT_SCIENCE.wr” as the core dataset. Click on menu “File -> Open supporting/QC file” and a dialog will present itself (Figure 3.9-1). Select a database that the supporting file is associated with, which is CHAVI_SETPOINT_SCIENCE in this case. Click on button “Support/QC file” to locate the text file containing the supporting/QC dataset (a file containing HWE results for cases in Figure 3.9-1). And then select the column for the SNP, and the columns to be included as supporting/QC information (P values for HWE as in Figure 3.9-1). Multiple-column selection is allowed. Click on the “OK” button and if the data is successfully loaded, a message box as in Figure 3.9-2 will present itself. If not, there may be unsupported data lines in file, for example, inconsistent column counts.
After the inclusion of supporting/QC files, the annotation for top hits (chapter 3.3) will automatically include columns for such information. For example, click on menu “Tools->Top hits” and annotate the top hits as discussed in chapter 3.3, the annotation results will be like Figure 3.9-3, with a column for HWE P value alongside each SNP.
Figure 3.9-1. To load a supporting/QC file. (Click to enlarge)
Figure 3.9-2. A supporting/ QC file is successfully loaded.
Figure 3.9-3. Briefly annotated top hits with supporting information. Circled are Hardy-Weinberg Equilibrium P values. (Click to enlarge)