as.MeDeComSet: as.MeDeComSet

In lutsik/MeDeCom: Decomposition of heterogeneous methylomes

as.MeDeComSet

Description

Function to convert object of type RefFreeCellMix to MeDeComSet

Usage

as.MeDeComSet(object, cg_subsets = 1, Ks = NULL, deviances = NULL,
  rss = NULL, m.orig = NULL, n.orig = NULL)

Arguments

object	An object of class RefFreeCellMix containing cell type deconvolution information, or a list of such objects.
cg_subsets	The indeces of the CpG subsets used in the analysis.
Ks	The values of K used in the analysis. If NULL, K is determined by the size of the matrices.
deviances	Optional argument specifying the deviances as computed with RefFreeCellMixArrayDevianceBoots.
rss	Optional argument specifying the residual sum of sqaures
m.orig	The original number of rows (CpGs) in the methylation matrix.
n.orig	The original number of columns (samples) in the methylation matrix.

Details

Since RefFreeCellMix only contains information on a single value for K, and does not contain any regularization (lambda), the corresponding parameters in the MeDeComSet are set to single numeric values. Furthermore, no information on goodness of fit (CVE, Fval) can be stored. If cg_subsets is not of length 1, an object containing multiple subsets is creared.

Value

An object of type MeDeComSet

lutsik/MeDeCom documentation built on Feb. 15, 2023, 11:32 a.m.