iCluster: 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, iCluster fits a regularized latent variable model based clustering that generates an integrated cluster assigment based on joint inference across data types

Usage

iCluster(datasets, k, lambda, scalar=FALSE, max.iter=50,epsilon=1e-3)

Arguments

datasets	A list object containing m data matrices representing m different genomic data types measured in a set of n samples. For each matrix, the rows represent samples, and the columns represent genomic features.
k	Number of subtypes.
lambda	Vector of length-m lasso penalty terms.
scalar	If TRUE, assumes scalar covariance matrix Psi. Default is FALSE.
max.iter	Maximum iteration for the EM algorithm.
epsilon	EM algorithm convegence criterion.

Value

A list with the following elements.

meanZ	Relaxed cluster indicator matrix.
beta	Coefficient matrix.
clusters	Cluster assigment.
conv.rate	Convergence history.

Author(s)

Ronglai Shen [e-mail]

References

Ronglai Shen, Adam Olshen, Marc Ladanyi. (2009). Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics 25, 2906-2912.

See Also

breast.chr17,plotiCluster, compute.pod

Examples

data(breast.chr17)
fit=iCluster(breast.chr17, k=4, lambda=c(0.2,0.2))
plotiCluster(fit=fit, label=rownames(breast.chr17[[2]]))
compute.pod(fit)

#library(gplots)
#library(lattice)
#col.scheme = alist()
#col.scheme[[1]] = bluered(256)
#col.scheme[[2]] = greenred(256)
#cn.image=breast.chr17[[2]]
#cn.image[cn.image>1.5]=1.5
#cn.image[cn.image< -1.5]= -1.5
#exp.image=breast.chr17[[1]]
#exp.image[exp.image>3]=3
#exp.image[exp.image< -3]=3
#plotHeatmap(fit, datasets=list(cn.image,exp.image), type=c("gaussian","gaussian"),
#  row.order=c(FALSE,FALSE), width=5, col.scheme=col.scheme)

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