Summarize the methylation states of Variable Methylated Loci (VML)

This function computes a representative methylation score for each Variable Methylated Locus (VML) in a dataset. It returns a data frame with the median methylation of each region per individual. For each VML in a dataset, returns a with the median methylation of that region (columns) per individual (rows) as representative score.

Usage

summarizeVML(VML_df, methylation_data)

Arguments

VML_df: A GRanges-like data frame. Must contain the following columns: "seqnames", "start", "end" and "probes" (containing lists as elements, where each contains a vector with the probes constituting the VML). This is the "VML" object returned by the findVML() function.
methylation_data: A data frame containing M or B values, with samples as columns and probes as rows. Row names must be the CpG probe IDs.

Value

A data frame with samples as rows, and VML as columns. The value inside each cell corresponds to the summarized methylation value of said VML in the corresponding individual. The column names correspond to the VML_index.

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., doParallel::registerDoParallel(4)). After that, the function can be run as usual.

Examples

## Find VML in test data
VML <- RAMEN::findVML(
   methylation_data = RAMEN::test_methylation_data,
   array_manifest = "IlluminaHumanMethylationEPICv1",
   cor_threshold = 0,
   var_method = "variance",
   var_distribution = "ultrastable",
   var_threshold_percentile = 0.99,
   max_distance = 1000
   )
#> Identifying Highly Variable Probes...
#> Identifying sparse Variable Methylated Probes
#> Identifying Variable Methylated Regions...
#> Applying correlation filter to Variable Methylated Regions...

## Summarize methylation states of the found VML
summarized_VML <- RAMEN::summarizeVML(
  VML_df = VML$VML,
  methylation_data = RAMEN::test_methylation_data
  )