Extract contiguous co-methylated genomic regions from a list of pre-defined genomic regions

CoMethAllRegions(
  dnam,
  betaToM = FALSE,
  method = c("pearson", "spearman"),
  rDropThresh_num = 0.4,
  minCpGs = 3,
  genome = c("hg19", "hg38"),
  arrayType = c("450k", "EPIC"),
  CpGs_ls,
  file = NULL,
  returnAllCpGs = FALSE,
  output = c("CpGs", "dataframe"),
  nCores_int = 1L,
  ...
)

Arguments

dnam: matrix (or data frame) of beta values, with row names = CpG IDs, column names = sample IDs. This is typically genome-wide methylation beta values.
betaToM: indicates if converting methylation beta values to mvalues
method: method for computing correlation, can be "spearman" or "pearson"
rDropThresh_num: threshold for min correlation between a cpg with sum of the rest of the CpGs
minCpGs: minimum number of CpGs to be considered a "region". Only regions with more than minCpGs will be returned.
genome: Human genome of reference hg19 or hg38
arrayType: Type of array, can be "450k" or "EPIC"
CpGs_ls: list where each item is a character vector of CpGs IDs. This should be CpG probes located closely on the array.
file: an RDS file with clusters of CpG locations (i.e. CpGs located closely to each other on the genome). This file can be generated by the WriteCloseByAllRegions function.
returnAllCpGs: When there is not a contiguous comethylated region in the inputting pre-defined region, returnAllCpGs = TRUE indicates outputting all the CpGs in the input regions (regardless of statistical significance), while returnAllCpGs = FALSE indicates not returning any CpGs not contained in comethylated clusters. Defaults to FALSE, and we provide this option for debugging purposes only.
output: a character vector of CpGs or a dataframe of CpGs along with rDrop info
nCores_int: Number of computing cores to be used when executing code in parallel. Defaults to 1 (serial computing).
...: Dots for additional arguments passed to the cluster constructor. See CreateParallelWorkers for more information.

Value

When output = "dataframe" is selected, returns a list of data frames, each with CpG (CpG name), Chr (chromosome number), MAPINFO (genomic position), r_drop (correlation between the CpG with rest of the CpGs), keep (indicator for co-methylated CpG), keep_contiguous (index for contiguous comethylated subregions). When output = "CpGs" is selected, returns a list, each item is a list of CpGs in the contiguous co-methylated subregion.

Details

There are two ways to input genomic regions for this function: (1) use CpGs_ls argument, or (2) use file argument. Examples of these files are in /inst/extdata/ folder of the package.

Examples

   data(betasChr22_df)


   CpGisland_ls <- readRDS(
     system.file(
       "extdata",
       "CpGislandsChr22_ex.rds",
       package = 'coMethDMR',
       mustWork = TRUE
     )
   )

   coMeth_ls <- CoMethAllRegions (
     dnam = betasChr22_df,
     betaToM = TRUE,
     method = "pearson",
     CpGs_ls = CpGisland_ls,
     arrayType = "450k",
     returnAllCpGs = FALSE,
     output = "CpGs"
   )
#> snapshotDate(): 2021-05-18
#> see ?sesameData and browseVignettes('sesameData') for documentation