getCIMLR: Get subtypes from CIMLR

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

Description

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

Usage

getCIMLR(
  data = NULL,
  N.clust = NULL,
  type = rep("gaussian", length(data)),
  cores.ratio = 0,
  verbose = TRUE
)

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.
cores.ratio	Ratio of the number of cores to be used when computing the multi-kernel.
verbose	A logic value to indicate if supressing progression.

Value

A list with the following components:

fit an object returned by CIMLR.

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

feat.res the results of features selection process.

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

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.

Examples

# There is no example and please refer to vignette.

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