run.rnb.ICA: run.rnb.ICA

In lutsik/DecompPipeline: Preparation pipeline for MeDeCom

Description

Performs ICA to remove the effect of a confounding factor from the methylation matrix

Usage

run.rnb.ICA(rnb.set, conf.factor, ica.setting = NULL, nmin = 10,
  nmax = 30, ntry = 1, thr.sd = 0, alpha.fact = 1e-10,
  type = "remove", ncores = 1, out.folder = NULL, save.report = F,
  alpha.feat = 0.01)

Arguments

rnb.set	An object of type RnBSet-class containing methylation information
conf.factor	A vector of column names in the sample annotation sheet of rnb.set representing confounding factors to be removed.
ica.setting	Optional argument. If specified a named vector of arguments to be used. Can be one of the following.
nmin	Minimum number of components to be used
nmax	Maximum number of components to be used
ntry	Further argument for runICA
thr.sd	Threshold for the standard deviation across samples. Only sites with a standard deviation larger than this threshold are kept. 0 deactivates filtering.
alpha.fact	Significance level for the factor
type	Analysis type to be performed. Can be either "remove" to remove the effect of the confounding factor or "keep" to export the sites that are linked to the confounding factor. Note that for "keep", the factor effect is not removed, but only reported.
out.folder	Folder to store ICA's output and diagnostic plots

Value

The modified rnb.set object with updated methylation values. The effect of the confouding factor is removed using independent component analysis (ICA).

Author(s)

Michael Scherer. ICA code was generated by Peter Nazarov and Tony Kamoa

lutsik/DecompPipeline documentation built on Oct. 13, 2019, 1:51 a.m.