rnb.execute.diffVar {RnBeads} | R Documentation

## rnb.execute.diffVar

### Description

This routine computes sites that are differentially variable between two sample groups specified as the column name in the phenotypic table.

### Usage

    rnb.execute.diffVar(
      rnb.set,
      pheno.cols = rnb.getOption("differential.comparison.columns"),
      region.types = rnb.region.types.for.analysis(rnb.set),
      columns.adj = rnb.getOption("covariate.adjustment.columns"),
      adjust.celltype = rnb.getOption("differential.adjustment.celltype"),
      disk.dump = rnb.getOption("disk.dump.big.matrices"),
      disk.dump.dir = tempfile(pattern = "diffMethTables_")
    )

### Arguments

`rnb.set` | Object of type `RnBSet` on which differential variability analysis should be conducted
`pheno.cols` | Column names used to define the classes, whose methylation variability should be compared with each other
`region.types` | Regions types to be used for the analysis. Defaults to the results given by rnb.region.types.for.analysis of the given RnBSet.
`columns.adj` | Column names or indices in the table of phenotypic information to be used for confounder adjustment in the differential variability analysis.
`adjust.celltype` | Flag indicating whether the resulting table should also contain estimated celltype contributions. See `rnb.execute.ct.estimation` for details.
`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`.

### Value

Object of type `RnBDiffMeth` containing information about the differential variability analysis.

### Author(s)

Michael Scherer

[Package RnBeads version 2.12.2 Index]