getMoCluster: Get subtypes from MoCluster

In xlucpu/MOVICS: Multi-Omics integration and VIsualization in Cancer Subtyping

Description

This function wraps the MoCluster (Multiple omics data integrative clustering) algorithm and provides standard output for 'getMoHeatmap()' and 'getConsensusMOIC()'.

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

data	List of matrices.
N.clust	Number of clusters.
type	Data type corresponding to the list of matrics, which can be gaussian, binomial or possion.
ncomp	An integer value to indicate the number of components to calculate. To calculate more components requires longer computational time.
method	A string value can be one of CPCA, GCCA and MCIA; CPCA by default.
option	A string value could be one of c('lambda1', 'inertia', 'uniform') to indicate how the different matrices should be normalized.
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.
center	A logical value to indicate if the variables should be centered. TRUE by default.
scale	A logical value to indicate if the variables should be scaled. TRUE by default.
clusterAlg	A string value to indicate the cluster algorithm for distance.

Value

A list with the following components:

fit an object returned by mbpca.

clust.res a data.frame storing sample ID and corresponding clusters.

feat.res the results of features selection process.

clust.dend a dendrogram of sample clustering.

mo.method a string value indicating the method used for multi-omics integrative clustering.

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.

Examples

# There is no example and please refer to vignette.

xlucpu/MOVICS documentation built on July 24, 2021, 9:23 p.m.