getLRAcluster: Get subtypes from LRAcluster

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

Description

This function wraps the LRAcluster (Integrated cancer omics data anlsysi by low rank approximation) algorithm and provides standard output for 'getMoHeatmap()' and 'getConsensusMOIC()'.

Usage

getLRAcluster(
  data = NULL,
  N.clust = NULL,
  type = rep("gaussian", length(data)),
  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; 'gaussian' by default.
clusterAlg	A string value to indicate the cluster algorithm for similarity matrix; 'ward.D' by default.

Value

A list with the following components:

fit an object returned by LRAcluster.

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

Wu D, Wang D, Zhang MQ, Gu J (2015). Fast dimension reduction and integrative clustering of multi-omics data using low-rank approximation: application to cancer molecular classification. BMC Genomics, 16(1):1022.

Examples

# There is no example and please refer to vignette.

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