Make MIRA-compatible data.tables using information from SummarizedExperiment-based classes

Packages that use SummarizedExperiment-based classes for DNA methylation data which could be converted with this function include "bsseq", "methylPipe", and "BiSeq" packages. Of the methylCountDF, coverageDF, and methylPropDF arguments, either methylPropDF must be given or both methylCountDF and coverageDF must be given. After that, whichever is not given will be calculated from the others. If coverageDF and methylCountDF are both not given, coverage will be assumed to be 1 at each site with a methylProp value. Acceptable formats for the three "DF" parameters include: data.frame, data.table, matrix, and DelayedMatrix classes. If converting a BSseq object, see ?bsseqToDataTable for a convenient wrapper of this function.

SummarizedExperimentToDataTable(coordinates, methylCountDF = NULL,
  coverageDF = NULL, methylPropDF = NULL, sample_names = NULL)

Arguments

coordinates	Coordinates for the methylation loci as a GRanges (or GPos) object (in same order as methylCountDF/coverageDF/methylPropDF, whichever is given). The start coordinate should be the coordinate of the cytosine.
methylCountDF	An object of matrix/data.frame/similar format that contains the number of reads with methylated C's for the loci in 'coordinates' argument. It should have one column per sample with rows that correspond to 'coordinates'.
coverageDF	An object of matrix/data.frame/similar format that contains the total number of reads for the loci in 'coordinates' argument. It should have one column per sample with rows that correspond to 'coordinates'.
methylPropDF	An object of matrix/data.frame/similar format that contains the total number of reads for the loci in 'coordinates' argument. It should have one column per sample with rows that correspond to 'coordinates'.
sample_names	A character vector with sample names in the same order as the columns of methylCountDF/coverageDF/methylPropDF samples in the columns

Value

MIRAFormatBSDTList A list of data.tables containing the methylation data. One data.table per sample with the column names: 'chr', 'start' (methylation coordinate), 'methylCount' (number of methylated reads), 'coverage' (total number of reads), and 'methylProp' (proportion of methylated reads). The order of the list is the order of samples in the columns of methylCountDF/coverageDF/methylPropDF. If sample names are explicitly given as input ('sample_names' argument) or can be derived from other arguments to the function then a named list will be returned.

Examples

data("exampleBSseqObj")
MIRAFormatBSDTList = SummarizedExperimentToDataTable(coordinates = bsseq::granges(exampleBSseqObj),
    methylCountDF = bsseq::getCoverage(BSseq = exampleBSseqObj, type = "M"),
    coverageDF = bsseq::getCoverage(BSseq = exampleBSseqObj, type = "Cov"),
    methylPropDF = bsseq::getMeth(BSseq = exampleBSseqObj, type = "raw"),
    sample_names = bsseq::sampleNames(exampleBSseqObj))
#> Loading required package: DelayedArray
#> Warning: there is no package called ‘DelayedArray’
#> Error in .requirePackage(package): unable to find required package ‘DelayedArray’