start.refreeewas.analysis: start.refreeewas.analysis

In lutsik/DecompPipeline: Preparation pipeline for MeDeCom

Description

This function executes RefFreeCellMix for the specified CpGs and the number of cell types K.

Usage

start.refreeewas.analysis(meth.data = NULL, rnb.set = NULL, cg_groups,
  Ks, work.dir = getwd(), factorviz.outputs = FALSE)

Arguments

meth.data	A matrix or data.frame containing methylation information. If NULL, methylation information needs to be provided through rnb.set
rnb.set	An object of type RnBSet-class containing methylation and sample meta information.
cg_groups	List of CpG indices used for the analysis. Can be computed by prepare_CG_subsets.
Ks	The number of cell types to be tested. Can be a single numeric value or an array of numbers.
work.dir	The working directory to be used.
factorviz.outputs	Flag indicating, if outputs should be stored to be compatible with FactorViz for data exploration

Value

An object of type MeDeComSet containing the results of the RefFreeCellMix experiment.

Author(s)

Michael Scherer

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