InfiniumClust: Tumor sample clustering from Infinium 450k array data

In InfiniumPurify: Estimate and Account for Tumor Purity in Cancer Methylation Data Analysis

Description

Clustering of tumor samples into subtypes accounting for tumor purity.

Usage

InfiniumClust(tumor.data, purity, K, maxiter = 100, tol = 0.001)

Arguments

tumor.data	numeric matrix of beta values for tumor samlpes. The rownames of tumor.data should be probe names of Infinium 450k array, and colnames should be names of tumor samples.
purity	purities for tumor samples. Could be estimated by getPurity, or user specified purities from other tools.
K	the number of clusters.
maxiter	the maximum number of iterations allowed. Default is 100.
tol	tolerance for convergence of EM iterations. Default is 0.001.

Details

An EM based statistical method for subtype classification based on DNA methylation data, while adjusting for tumor purity.

Value

InfiniumClust returns a list consisting oflikelihood tol.ll and membership matrix Z.

tol.ll	total log-likelihood of converged EM algorithm.
Z	the membership matrix, where row corresponds to tumor samples and column corresponds to K clusters.

Author(s)

Xiaoqi Zheng [e-mail] and Hao Wu [e-mail]

References

W. Zhang, H. Feng, H. Wu and X. Zheng (2016). Tumor purity improves cancer subtype classification from DNA methylation data. Submitted.

Examples

## load example data
data(beta.emp)
normal.data <- beta.emp[,1:21]
tumor.data <- beta.emp[,22:31]

## estimate tumor purity
purity <- getPurity(tumor.data = tumor.data,tumor.type= "LUAD")

## cluster tumor samples accounting for tumor purity
out <- InfiniumClust(tumor.data,purity,K=3, maxiter=5, tol=0.001)

Example output

Loading required package: matrixStats
The number of tumor samples is: 10
Calculating tumor purity ...
Iter 1 , diff= 0.1287939 
Iter 2 , diff= 0.1157339 
Iter 3 , diff= 0.0595212 
Iter 4 , diff= 0.05458117 
Iter 5 , diff= 0.03671596 
# of clusters chosen: 3 
Probability of each cluster =  0.3 0.4 0.3 
Total log-likelihood =  1030.146 

InfiniumPurify documentation built on May 1, 2019, 9:23 p.m.