rnb.execute.computeDiffMeth {RnBeads} | R Documentation

## rnb.execute.computeDiffMeth

### Description

computes differential methylation

### Usage

    rnb.execute.computeDiffMeth(
      x,
      pheno.cols,
      region.types = rnb.region.types.for.analysis(x),
      covg.thres = rnb.getOption("filtering.coverage.threshold"),

        pheno.cols.all.pairwise = rnb.getOption("differential.comparison.columns.all.pairwise"),
      columns.pairs = rnb.getOption("columns.pairing"),
      columns.adj = rnb.getOption("covariate.adjustment.columns"),
      adjust.sva = rnb.getOption("differential.adjustment.sva"),
      pheno.cols.adjust.sva = rnb.getOption("inference.targets.sva"),
      adjust.celltype = rnb.getOption("differential.adjustment.celltype"),
      skip.sites = !rnb.getOption("analyze.sites"),
      disk.dump = rnb.getOption("disk.dump.big.matrices"),
      disk.dump.dir = tempfile(pattern = "diffMethTables_"),
      ...
    )

### Arguments

`x` | RnBSet object
`pheno.cols` | column names of the pheno slot in `x` on which the dataset should be partitioned. Those columns are required to be factors or logical. In case of factors, each group in turn will be compared to all other groups
`region.types` | which region types should be processed for differential methylation
`covg.thres` | coverage threshold for computing the summary statistics. See `computeDiffTab.extended.site` for details.
`pheno.cols.all.pairwise` | integer or character vector specifying the colomns of `pheno(x)` on which all pairwise comparisons should be conducted. A value of `NULL` (default) indicates no columns.
`columns.pairs` | argument passed on to `rnb.sample.groups`. See its documentation for details.
`columns.adj` | Column names or indices in the table of phenotypic information to be used for confounder adjustment in the differential methylation analysis.
`adjust.sva` | flag indicating whether the adjustment table should also contain surrogate variables (SVs) for the given target variable.
`pheno.cols.adjust.sva` | Column names or indices in the table of phenotypic information to be used for SVA adjustment in the differential methylation analysis.
`adjust.celltype` | flag indicating whether the resulting table should also contain estimated celltype contributions. See `rnb.execute.ct.estimation` for details.
`skip.sites` | flag indicating whether differential methylation in regions should be computed directly and not from sites. This leads to skipping of site-specific differential methylation
`disk.dump` | Flag indicating whether the resulting differential methylation object should be file backed, ie.e the matrices dumped to disk
`disk.dump.dir` | disk location for file backing of the resulting differential methylation object. Only meaningful if `disk.dump=TRUE`. must be a character specifying an NON-EXISTING valid directory.
`...` | arguments passed on to binary differential methylation calling. See `computeDiffTab.extended.site` for details.

### Value

an `RnBDiffMeth` object. See class description for details.

### Author(s)

Fabian Mueller

### Examples

    library(RnBeads.hg19)
    data(small.example.object)
    logger.start(fname=NA)
    dm <- rnb.execute.computeDiffMeth(rnb.set.example,pheno.cols=c("Sample_Group","Treatment"))
    get.comparisons(dm)

[Package RnBeads version 2.12.2 Index]