The main menu consists of four menu groups: File, Tools, Database, Window, and About. The menu items will be activated (colored in black instead of gray) when the conditions for performing the corresponding functions are satisfied.
- Open WGA result set: will load a “.wr” (pre-annotation) or “.wga” (post-annotation) file;
- Open external data file: will load a text-based WGA result set, including outputs from PLINK (Purcell et al. 2007) . See chapter 3.2;
- Open an example dataset: will load an example dataset released with WGAViewer. In this current version we use our recently completed study on host control of HIV-1 viral load during the asymptomatic set point period (Fellay et al. 2007) as example datasets. See chapter 3.1;
- New work: will start a new annotation project;
- Open saved work: will load the post-annotation file (.wga). For example see chapter 3.1;
- Open supporting/QC file: will load supporting/QC files to help interpret WGA results. See chapter 3.9;
- Save genome overview image: will save “Genome overview” tabbed panel as an image file. See chapter 3.6;
- Save chromosome browser image: will save “Chromosome” tabbed panel as an image file. See chapter 3.6;
- Save gene context image: will save “Gene context” tabbed panel as an image file. See chapter 3.6;
- Save SNP annotation image: will save “SNP” tabbed panel as an image file. See chapter 3.6;
- Recent files: includes a list of recently opened files. Click to open them again;
- Exit: will exit WGAViewer.
Figure 3.13.1-1. File menu
- Make input file for WGAViewer: will make text-based .wr file for WGAViewer from text-based WGA result set. See chapter 3.2;
- Top hits: will sort the dataset, find and annotate the top hits with specified number. See chapter 3.3;
- Find a gene: will locate and annotate a gene region with specified span in the loaded WGA result set. See chapter 3.4;
- Find a SNP: will check the coverage of specified SNP and its LD proxies in the loaded WGA result set. See chapter 3.5;
- Annotate a SNP: will annotate a SNP not necessarily based a WGA result set. See chapter 3.11.2;
- Q-Q plot: will perform a Q-Q plot and calculate a lambda value to inspect the effects of population stratification, and to visually inspect how the top hit P values depart from the random distribution. See chapter 3.7;
- Linkage disequilibrium test: will perform LD test for a list of SNPs using HapMap (The International HapMap Consortium. 2007) data, without detailed information necessary for inputs. See chapter 3.11.3;
- GENEVAR: test for genotype-expression association: will perform a genotype-gene expression association test based on specified SNPs and genes, using Sanger Institute GENEVAR database (Stranger et al. 2005) and HapMap database (The International HapMap Consortium. 2007) .
Figure 3.13.1-2. Tools menu
- Released database with this package: will load the released .wga database with this current WGAViewer package;
- MIDAS online: will access the Mart for IGSP Data from Association Studies database. See chapter 3.10.
- Database manager: will plot all data points from all core and reference databases in a separate window, and allows an interactive zoom in/out as well as annotation. See chapter 3.8.1;
- Database cross reference: will search for all SNPs that show concurrent association signals at a specified level in core and all reference databases. This function requires at least one reference database to be loaded. See chapter 3.8.2;
- Database plotter: will plot all data points from all core and reference databases in a separate window, and allows an interactive zoom in/out as well as annotation. See also chapter 3.8.1;
Figure 3.13.1-3. Database menu
This menu allows a revisit to the saved annotation results after the related data windows are closed. These menu items will be activated if such annotation results are already available.
1. SNP finder: will show the results from “Find a SNP”. See menu “Tools-> Find a SNP” and chapter 3.5;
2. Top hits viewer: will show the annotation results for top hits. See menu “Tools->Top hits” and chapter 3.3;
3. Cross reference viewer: will show the results for database cross reference. See menu “Database-> Database cross reference” and chapter 3.8.2;
Figure 3.13.1-4. Window menu
- Help: will display help window;
- Check for Updates: will check and download the latest online WGAViewer version. The WGAViewer software needs a restart to take effect the updates;
- About this software: will display software information (Figure 3.13.1-6).
Figure 3.13.1-5. About menu
Figure 3.13.1-6. About this software.