Combine 5-base methylation and variant data

The Combine 5-base methylation and variant data task enables users to combine annotated differentially methylated regions (DMRs) and annotated variants, for dual-omics insights in DNA Methylation Prep data analysis.

Running Combine 5-base methylation and variant data

The Combine 5-base methylation and variant data task expects annotated DMRs and annotated variants data within the same analysis. This task can be invoked at either Annotated regions data node or Annotated variants data node.

• Click Annotated regions or Annotated variants data node.

• Click Combine multiomics data section in the context-sensitive task menu.

• Click Combine 5-base methylation and variant data.

• Click Select data node to select another data node (Annotated variants or Annotated regions) for intersection or union.

• Data nodes that are selectable for combine are in blue. In example below, Annotated regions data node from the methylation analysis branch are selected.

• Select intersection or union to combine methylation and variant data, then click Finish.

  • Intersection: Use gene ID to intersect DMRs and variants. Every intersected variant and DMR will be reported in an individual row in task report.

  • Union: Report intersection (by gene ID) result and also variants that overlap DMR by specified distance (default is +/- 1000bp).

Task output

When complete, double-click on 5-base methylation and variants data node to open result. The task report is similar to the Summarized cohort mutations task report, with an additional column Origin to indicate if result in a row is present in both methylation and variant data (VC, DMR), or variant data only (VC), or methylation data only (DMR).