Filter colon cancer samples by Silhouette width

Description

This function computes Silhouette widths for the 90 colon cancer samples.

Usage

filterSamples(sdat, uniGenes, clus)
figSilh(silh)

Arguments

Details

Silhouette width was computed to identify the most representative samples within each cluster. Samples with positive silhouette width were retained to build the PAM classifier.

Value

This function will return a list including sdat.f (a matrix of median centered expression values of top variable genes for selected samples), clus.f (a numeric vector of cluster labels for selected cancer samples) and silh (an object of class silhouette).

Author(s)

Xin Wang xw264@cam.ac.uk

References

De Sousa E Melo, F. and Wang, X. and Jansen, M. et al. Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion. accepted

Rousseeuw, Peter J (1987). Silhouettes: a graphical aid to the interpretation and validation of cluster analysis Journal of computational and applied mathematics, 20, 53-65.

See Also

selTopVarGenes

Examples

data(uniGenes, package="DeSousa2013")
data(dat, package="DeSousa2013")
data(conClust, package="DeSousa2013")
samp.f <- filterSamples(sdat, uniGenes, clus)
figSilh(samp.f$silh)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(DeSousa2013)

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DeSousa2013/filterSamples.Rd_%03d_medium.png", width=480, height=480)
> ### Name: filterSamples
> ### Title: Filter colon cancer samples by Silhouette width
> ### Aliases: filterSamples figSilh
> 
> ### ** Examples
> 
> data(uniGenes, package="DeSousa2013")
> data(dat, package="DeSousa2013")
> data(conClust, package="DeSousa2013")
> samp.f <- filterSamples(sdat, uniGenes, clus)
> figSilh(samp.f$silh)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>