WGAViewer

Figure 3.13.2-1. Tool bar

From up to down, these tool buttons are:

•  Create new work: equivalent to menu item “File->New work”;

•  Open project file: will load a “.wr” (pre-annotation) or “.wga” (post-annotation) file. Equivalent to menu item “File->Open WGA result set”;

•  Save work session: will save the work session to a binary “.wga” file with all interactive features included. Equivalent to menu item “File->Save work”;

•  Top hits: will sort the dataset, find and annotate the top hits with specified number. Equivalent to menu item “Tools -> Top hits”. See also chapter 3.3;

•  Find a gene: will locate and annotate a gene region, with specified span. Equivalent to menu item “Tools->Find a gene”. See also chapter 3.4;

•  Find a SNP: will check the coverage of specified SNP and its LD proxies in the loaded WGA data set. Equivalent to menu item “Tools->Find a SNP”. See also chapter 3.5;

•  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. Equivalent to menu item “Tools->Q-Q plot”. See also chapter 3.7;

•  Database manager: will allow a user to load, remove, and add description to core and reference databases. One also may use this interface to plot database and access MIDAS database. Equivalent to menu item “Database -> Database manager”. See also chapters 3.8 and 3.10;

•  Cross reference: will search for all SNPs that show concurrent association signals at a specified level in core and all reference databases. Equivalent to menu item “Database -> Database cross reference”. See also 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. Equivalent to menu “Tools -> Databases plotter”. See also chapter 3.8.1;

•  Mart for IGSP Data from Association Studies (MIDAS): will access the MIDAS online database. See also chapter 3.10.

•  Help: will bring up a help window for each panel that currently has the focus.