% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/getCIMLR.R

\name{getCIMLR}

\alias{getCIMLR}

\title{Get subtypes from CIMLR}

\usage{

getCIMLR(

  data = NULL,

  N.clust = NULL,

  type = rep("gaussian", length(data)),

  cores.ratio = 0,

  verbose = TRUE

)

}

\arguments{

\item{data}{List of matrices.}

\item{N.clust}{Number of clusters.}

\item{type}{Data type corresponding to the list of matrics, which can be gaussian, binomial or possion.}

\item{cores.ratio}{Ratio of the number of cores to be used when computing the multi-kernel.}

\item{verbose}{A logic value to indicate if supressing progression.}

}

\value{

A list with the following components:

        \code{fit}       an object returned by \link[CIMLR]{CIMLR}.

        \code{clust.res} a data.frame storing sample ID and corresponding clusters.

        \code{feat.res}  the results of features selection process.

        \code{mo.method} a string value indicating the method used for multi-omics integrative clustering.

}

\description{

This function wraps the CIMLR (Cancer Integration via Multikernel Learning) algorithm and provides standard output for `getMoHeatmap()` and `getConsensusMOIC()`.

}

\examples{

# There is no example and please refer to vignette.

}

\references{

Ramazzotti D, Lal A, Wang B, Batzoglou S, Sidow A (2018). Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival. Nat Commun, 9(1):4453.

}