Browsing Linkage Disequilibrium

Browsing Linkage Disequilibrium

The screenshot below shows the data quality page for the input file. Any time a linkage or HapMap file is loaded, Haploview computes some quick quality metrics which can be used to screen markers. All of the ratings are discussed in depth in the documentation. Here we can see that all 20 markers in this dataset pass the default cutoffs. These cutoffs can be adjusted on this page and individual markers can be added or removed to the subsequent analysis by clicking the checkboxes in the "Rating" column. All of the other analyses are carried out only on those markers checked on this pane.


In order to browse the LD structure of your data, either select LD Plot from the Display menu or click on the LD Plot tab in the upper left area of the display. The data should look like the following screenshot:


The LD display allows you to examine your data in a number of ways. Detailed LD statistics for any comparison can be brought up by right-clicking on any box. Right clicking on a marker number shows it's name and minor allele frequency. You can zoom in and out using the zoom option in the Display menu (especially helpful for big datasets). Large datasets also show a mini-map in the lower left corner which is helpful for navigating. The color scheme and marker spacing for the LD display can be adjusted in the "Display" menu. A key for the color schemes is at the far right of the menu bar.