Summarize the methylation states of Variable Methylated Regions (VMRs)

For each VMR in a dataset, returns an object with the median methylation of that region per individual as representative score.

Usage

summarizeVMRs(VMRs_df, methylation_data)

Arguments

VMRs_df

A GRanges object converted to a data frame. Must contain the following columns: "seqnames", "start", "end" (all of which are produced automatically when doing the object conversion) and "probes" (containing a list where each element contains a vector with the probes constituting the VMR).

methylation_data

A data frame containing M or B values, with samples as columns and probes as rows.

Value

A data frame with samples as rows, and VMRs as columns. The value inside each cell corresponds to the summarized methylation value of said VMR in the corresponding individual. The column names correspond to the VMR_index, which is created if not already existing based on the rownames of the VMR_df.

Details

This function supports parallel computing for increased speed. To do so, you have to set the parallel backend in your R session BEFORE running the function (e.g., doFuture::registerDoFuture()) and then the evaluation strategy (e.g., future::plan(multisession)). After that, the function can be run as usual.