Get Regional Methylation

The Get Regional Methylation task uses an annotation file to generate a regions-by-samples count matrix from CpG methylation counts data. In a region, methylation counts of all CpG sites within the region are averaged to produce a count value in the regions-by-samples count matrix. To invoke Get Regional Methylation task,

• Click on 5-base Methylation data node, choose Region analysis > Get Regional Methylation.

• Select an annotation model from Assembly and Annotation model drop-down, then click Finish.

For many model organisms, the Connected Multiomics supports automatic downloads of gene/feature annotation models from commonly used sources (e.g. ENSEMBL, GENCODE). If the annotation model you want to use does not appear in the Annotation model drop down, click Add Annotation model from the Annotation model drop down. In the Add annotation file pop-up dialog, choose an annotation model you want to download from the Annotation model drop-down, then click Create to add the selected annotation model.

The Get Regional Methylation task produces a Get Regional Methylation task node and a Regional methylation data node. You can annotate the Regional methylation data node with genes information using Annotate Regions task and subsequently perform exploratory analysis such as PCA.