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Compute the median probe methylation pearson correlation for each Variable Methylated Region (VMR).

Source: R/medCorVMR.R
medCorVMR.Rd

This function will take a GRanges object converted into a data frame, where each row corresponds to a Variable Methylated Region. Then, it computes the pairwise correlation of the probes of each VMR and reports its median pairwise probe correlation.

Usage

medCorVMR(VML, methylation_data)

Arguments

VML

GRanges object. Must contain a metadata column named "probes", where each element contains a vector with the probes constituting the VML.

methylation_data

A data frame containing M or B values, with samples as columns and probes as rows. Data is expected to have already passed through quality control and cleaning steps. Rows must be the CpG probe IDs.

Value

A GRanges object like VML with an extra column per region containing the median pairwise correlation.

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. It is recommended to also set options(future.globals.maxSize= +Inf).

Examples

# Evaluate sequentially
foreach::registerDoSEQ()
# Create a VML object
VML <- GenomicRanges::GRanges(seqnames = c("chr21", "chr21"),
      ranges = IRanges::IRanges(start = c(10861376, 10862171),
                       end = c(10862507, 10883548)),
      probes = I(list(
        c("cg15043638", "cg18287590", "cg17975851"),
        c("cg13893907", "cg17035109", "cg06187584")))
      )

# Compute median correlation for each VMR
medCorVMR(VML = VML, methylation_data = RAMEN::test_methylation_data)
#> GRanges object with 2 ranges and 2 metadata columns:
#>       seqnames            ranges strand |                           probes
#>          <Rle>         <IRanges>  <Rle> |                           <list>
#>   [1]    chr21 10861376-10862507      * | cg15043638,cg18287590,cg17975851
#>   [2]    chr21 10862171-10883548      * | cg13893907,cg17035109,cg06187584
#>       median_correlation
#>                <numeric>
#>   [1]           0.727516
#>   [2]           0.746814
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths