sigclustTest: A statistical method for testing the significance of...

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/Valiation.R

Description

SigClust (Statistical significance of clustering) is a statistical method for testing the significance of clustering results. SigClust can be applied to assess the statistical significance of splitting a data set into two clusters. SigClust studies whether clusters are really there, using the 2-means (k = 2) clustering index as a statistic. It assesses the significance of clustering by simulation from a single null Gaussian distribution. Null Gaussian parameters are estimated from the data. Here we apply the SigClust to assess the statistical significance of pairwise subtypes. "sigclust" package should be installed.

Usage

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sigclustTest(Data, group, nsim = 1000, nrep = 1, icovest = 1)

Arguments

Data

A data matrix representing the genomic data measured in a set of samples. For the matrix, the rows represent the genomic features, and the columns represents the samples.

group

The subtypes label of each sample

nsim

This is a parameter inherited from sigclust() in "sigclust" Package. Number of simulated Gaussian samples to estimate the distribution of the clustering index for the main p-value computation.

nrep

This is a parameter inherited from sigclust() in "sigclust" Package. Number of steps to use in 2-means clustering computations (default=1, chosen to optimize speed).

icovest

This is a parameter inherited from sigclust() in "sigclust" Package. Covariance estimation type: 1. Use a soft threshold method as constrained MLE (default); 2. Use sample covariance estimate (recommended when diagnostics fail); 3. Use original background noise threshold estimate (from Liu, et al, (2008)) ("hard thresholding").

Value

A matrix indicates the p-value between pairwise subtypes.

Author(s)

Xu,Taosheng taosheng.x@gmail.com,Thuc Le Thuc.Le@unisa.edu.au

References

Liu, Yufeng, Hayes, David Neil, Nobel, Andrew and Marron, J. S, 2008, Statistical Significance of Clustering for High-Dimension, Low-Sample Size Data, Journal of the American Statistical Association 103(483) 1281-1293.
Huang, Hanwen, Yufeng Liu, Ming Yuan, and J. S. Marron. "Statistical Significance of Clustering Using Soft Thresholding." Journal of Computational and Graphical Statistics, no. just-accepted (2014): 00-00.

See Also

sigclust

Examples

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data(GeneExp)
data(miRNAExp)
data(time)
data(status)
GBM=list(GeneExp=GeneExp,miRNAExp=miRNAExp)
result=ExecuteSNF(GBM, clusterNum=3, K=20, alpha=0.5, t=20)
group=result$group
sigclust1=sigclustTest(miRNAExp,group, nsim=500, nrep=1, icovest=3)
sigclust2=sigclustTest(miRNAExp,group, nsim=1000, nrep=1, icovest=1)

xtsvm/CancerSubtypes documentation built on May 4, 2019, 1:26 p.m.