To illustrate this software, 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 an example (CHAVI_SETPOINT_SCIENCE). All the illustrations in this documentation are based on this example.
To load this example, click on menu “File->Open an example dataset” (Figure 3.1-1). Two types of datasets are released with this package. One is the pre-annotation dataset (.wr file, text-based) and the other is the post-annotation dataset (.wga file, binary). Figure 3.1-1 shows that the annotated dataset is selected, and Figure 3.1-2 shows the window after this example dataset is loaded. Figure 3.1-2 also shows two of the genome-wide significant hits (red vertical lines) that we recently reported (Fellay et al. 2007) . This real dataset is based on the Illumina HumanHap 550K SNP chip.
For demonstrating the usage of multiple databases discussed later in this user guide, we also include a simulated dataset (Illumina_HumanHap300_sim.wr) in this software package. This is a simulated set based on Illumina HumanHap 300K.
Figure 3.1-1 Load example dataset. (Click to enlarge)
Figure 3.1-2 Example dataset loaded. (Click to enlarge)