rnb.execute.computeDiffMeth {RnBeads} | R Documentation |
computes differential methylation
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_"), ... )
x |
RnBSet object |
pheno.cols |
column names of the pheno slot in |
region.types |
which region types should be processed for differential methylation |
covg.thres |
coverage threshold for computing the summary statistics. See |
pheno.cols.all.pairwise |
integer or character vector specifying the colomns of |
columns.pairs |
argument passed on to |
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 |
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 |
... |
arguments passed on to binary differential methylation calling. See |
an RnBDiffMeth
object. See class description for details.
Fabian Mueller
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)