getCOCA: Get subtypes from COCA

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

Description

This function wraps the COCA (Cluster-of-Clusters Analysis) algorithm and provides standard output for 'getMoHeatmap()' and 'getConsensusMOIC()'.

Usage

getCOCA(
  data = NULL,
  N.clust = NULL,
  type = rep("gaussian", length(data)),
  methods = "hclust",
  distances = "euclidean"
)

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.
methods	A string vector storing the names of clustering methods to be used to cluster the observations in each subdataset.
distances	A string vector storing the name of distances to be used in the clustering step for each subdataset.

Value

A list with the following components:

fit an object returned by coca.

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

clust.dend a dendrogram of sample clustering.

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

References

Hoadley KA, Yau C, Wolf DM, et al (2014). Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell, 158(4):929-944.

Examples

# There is no example and please refer to vignette.

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