rnb.execute.computeDiffMeth: rnb.execute.computeDiffMeth

In RnBeads: RnBeads

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)

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