MixtureModel_Biv: The MixtureModel_Biv function

In mpru/BIMEGA: BIMEGA: BIvariate Methylation and Expression GAussian mixture model

Description

Internal. Prepares all the structures to store the results and calls in a foreach loop a function that fits the mixture model in each gene.

Usage

MixtureModel_Biv(METcancer, METnormal, MAcancer, MAnormal = NULL,
  FunctionalGenes, NoNormalMode = FALSE)

Arguments

METcancer	matrix with methylation data for cancer samples (genes in rows, samples in columns).
METnormal	matrix with methylation data for normal samples (genes in rows, samples in columns).
MAcancer	matrix with gene expression data for cancer samples (genes in rows, samples in columns).
MAnormal	optional matrix with gene expression data for normal samples (genes in rows, samples in columns).
FunctionalGenes	vector with genes names to be considered for the mixture models.
NoNormalMode	logical, if TRUE no comparison to normal samples is performed. Defaults to FALSE.

Value

MethylationStates matrix of DM values, with driver genes in the rows and samples in the columns.

NrComponents matrix with the number of components identified for each driver gene.

Models list with the mixture model fitted for each driver gene.

MethylationDrivers character vector with the genes found by BIMEGA as differentially methylated and transcriptionally predictive (driver genes).

MixtureStates a list with a matrix for each driver gene containing the DM values.

Classifications a vector indicating to which component each sample was assigned.

mpru/BIMEGA documentation built on May 23, 2019, 6:34 a.m.