iClusterPlus: Integrative clustering of multiple genomic data types

In iClusterPlus: Integrative clustering of multi-type genomic data

Description

Given multiple genomic data types (e.g., copy number, gene expression, DNA methylation) measured in the same set of samples, iClusterPlus fits a regularized latent variable model based clustering that generates an integrated cluster assignment based on joint inference across data types

Usage

iClusterPlus(dt1,dt2=NULL,dt3=NULL,dt4=NULL,
	type=c("gaussian","binomial","poisson","multinomial"),
 	K=2,alpha=c(1,1,1,1),lambda=c(0.03,0.03,0.03,0.03),
	n.burnin=100,n.draw=200,maxiter=20,sdev=0.05,eps=1.0e-4)

Arguments

dt1	A data matrix. The rows represent samples, and the columns represent genomic features.
dt2	A data matrix. The rows represent samples, and the columns represent genomic features.
dt3	A data matrix. The rows represent samples, and the columns represent genomic features.
dt4	A data matrix. The rows represent samples, and the columns represent genomic features.
type	Data type, which can be gaussian, binomial, poisson, multinomial.
K	The number of eigen features. Given K, the number of cluster is K+1.
alpha	Vector of elasticnet penalty terms. At this version of iClusterPlus, elasticnet is not used. Therefore, all the elements of alpha are set to 1.
lambda	Vector of lasso penalty terms.
n.burnin	Number of MCMC burnin.
n.draw	Number of MCMC draw.
maxiter	Maximum iteration for the EM algorithm.
sdev	standard deviation of random walk proposal.
eps	Algorithm convergence criterion.

Value

A list with the following elements.

alpha	Intercept parameter.
beta	Information parameter.
clusters	Cluster assignment.
centers	Cluster center.
meanZ	Latent variable.
BIC	Bayesian information criterion.
dev.ratio	see dev.ratio defined in glmnet package.
dif	absolute difference for the parameters in the last and next-to-last iterations.

Author(s)

Qianxing Mo [e-mail],Ronglai Shen, Sijian Wang

References

Qianxing Mo, Sijian Wang, Venkatraman E. Seshan, Adam B. Olshen, Nikolaus Schultz, Chris Sander, R. Scott Powers, Marc Ladanyi, and Ronglai Shen. (2013). Pattern discovery and cancer gene identification in integrated cancer genomic data. Proc. Natl. Acad. Sci. USA. 110(11):4245-50.

See Also

plotiCluster,iCluster, compute.pod

Examples

# see iManual.pdf

Example output

Loading required package: parallel

iClusterPlus documentation built on Nov. 8, 2020, 8:01 p.m.