Description of LD Diagram

 

LD Figure

Each vertical line represents a CpG site. The number aligned to the right of each line represents that CpG's ID. There is key below the diagram that reports the coordinate of the CpG ID represented in the diagram. Each diamond represents an r2 value between two CpG sites. Higher r2 values, which mean more organized methylation, are represented by more intense color. Gray diamonds represent not r2 information. These r2 diagrams form a complete triangle but to save space, CpGs pairs that contain not read information are not shown.

LD Table

The first column contains a number that is also displayed in the diagram above. The second column reveals that coordinate of the CpG site associated with that ID. If a CpG has any pairwise r2 values greater than .3, which we considered significant, it is highlighted in blue.