getiClusterBayes: Get subtypes from iClusterBayes

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

Description

This function wraps the iClusterBayes (Integrative clustering by Bayesian latent variable model) algorithm and provides standard output for 'getMoHeatmap()' and 'getConsensusMOIC()'.

Usage

getiClusterBayes(
  data = NULL,
  N.clust = NULL,
  type = rep("gaussian", length(data)),
  n.burnin = 18000,
  n.draw = 12000,
  prior.gamma = rep(0.5, length(data)),
  sdev = 0.05,
  thin = 3
)

Arguments

data	List of matrices with maximum of 6 subdatasets.
N.clust	Number of clusters.
type	Data type corresponding to the list of matrics, which can be gaussian, binomial or possion.
n.burnin	An integer value to indicate the number of MCMC burnin.
n.draw	An integer value to indicate the number of MCMC draw.
prior.gamma	A numerical vector to indicate the prior probability for the indicator variable gamma of each subdataset.
sdev	A numerical value to indicate the standard deviation of random walk proposal for the latent variable.
thin	A numerical value to thin the MCMC chain in order to reduce autocorrelation.

Value

A list with the following components:

fit an object returned by iClusterBayes.

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

Mo Q, Shen R, Guo C, Vannucci M, Chan KS, Hilsenbeck SG (2018). A fully Bayesian latent variable model for integrative clustering analysis of multi-type omics data. Biostatistics, 19(1):71-86.

Examples

# There is no example and please refer to vignette.

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