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+++ b/man/getMoCluster.Rd
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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/getMoCluster.R
+\name{getMoCluster}
+\alias{getMoCluster}
+\title{Get subtypes from MoCluster}
+\usage{
+getMoCluster(
+  data = NULL,
+  N.clust = NULL,
+  type = rep("gaussian", length(data)),
+  ncomp = NULL,
+  method = "CPCA",
+  option = "lambda1",
+  k = 10,
+  center = TRUE,
+  scale = TRUE,
+  clusterAlg = "ward.D"
+)
+}
+\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{ncomp}{An integer value to indicate the number of components to calculate. To calculate more components requires longer computational time.}
+
+\item{method}{A string value can be one of CPCA, GCCA and MCIA; CPCA by default.}
+
+\item{option}{A string value could be one of c('lambda1', 'inertia', 'uniform') to indicate how the different matrices should be normalized.}
+
+\item{k}{A numeric value to indicate the absolute number (if k >= 1) or the proportion (if 0 < k < 1) of non-zero coefficients for the variable loading vectors. It could be a single value or a vector has the same length as x so the sparsity of individual matrix could be different.}
+
+\item{center}{A logical value to indicate if the variables should be centered. TRUE by default.}
+
+\item{scale}{A logical value to indicate if the variables should be scaled. TRUE by default.}
+
+\item{clusterAlg}{A string value to indicate the cluster algorithm for distance.}
+}
+\value{
+A list with the following components:
+
+        \code{fit}        an object returned by \link[mogsa]{mbpca}.
+
+        \code{clust.res}  a data.frame storing sample ID and corresponding clusters.
+
+        \code{feat.res}   the results of features selection process.
+
+        \code{clust.dend} a dendrogram of sample clustering.
+
+        \code{mo.method}  a string value indicating the method used for multi-omics integrative clustering.
+}
+\description{
+This function wraps the MoCluster (Multiple omics data integrative clustering) algorithm and provides standard output for `getMoHeatmap()` and `getConsensusMOIC()`.
+}
+\examples{
+# There is no example and please refer to vignette.
+}
+\references{
+Meng C, Helm D, Frejno M, Kuster B (2016). moCluster: Identifying Joint Patterns Across Multiple Omics Data Sets. J Proteome Res, 15(3):755-765.
+}