rnb.execute.diffVar: rnb.execute.diffVar

In RnBeads: RnBeads

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

RnBeads documentation built on March 3, 2021, 2 a.m.