Classifying the AMC samples

Description

These functions classify and visualize the 90 AMC colon cancer samples.

Usage

pamClassify(datsel, signature, pam.rslt, thresh, postRth=1)
figClassify(AMC_CRC_clinical, pred, clu.pred, sdat.sig, gclu.f, nam.ord)

Arguments

Details

The function pamClassify classifies the 90 AMC colon cancer samples using the gene expression based classifier built by PAM. The function figClassify generates classification results with a heatmap of median centred expression values across samples, a track indicating classification probabilities, as well as a track indicating relapse of patients.

Value

This function pamClassify will return a list including sdat.sig (a numeric matrix of expression values of signature genes for the 90 samples), pred (a numeric matrix of posterior probabilities for samples to be classified to subtypes), nam.ord (a character vector of samples ordered by their classification probabilies for visualization), gclu.f (result of hierarchical clustering on the expression of signature genes for visualization).

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

See Also

buildClassifier

Examples

data(AMC, package="DeSousa2013")
data(dat, package="DeSousa2013")
data(uniGenes, package="DeSousa2013")
data(diffGenes.f, package="DeSousa2013")
data(classifier, package="DeSousa2013")
datsel <- sdat[names(uniGenes), ]
rownames(datsel) <- uniGenes	
datsel <- datsel[diffGenes.f, ]
pamcl <- pamClassify(datsel, signature, pam.rslt, thresh, postRth=1)
figClassify(AMC_CRC_clinical, pamcl$pred, pamcl$clu.pred, pamcl$sdat.sig, 
pamcl$gclu.f, pamcl$nam.ord)

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.

R is a collaborative project with many contributors.
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/pamClassify.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pamClassify
> ### Title: Classifying the AMC samples
> ### Aliases: pamClassify figClassify
> 
> ### ** Examples
> 
> data(AMC, package="DeSousa2013")
> data(dat, package="DeSousa2013")
> data(uniGenes, package="DeSousa2013")
> data(diffGenes.f, package="DeSousa2013")
> data(classifier, package="DeSousa2013")
> datsel <- sdat[names(uniGenes), ]
> rownames(datsel) <- uniGenes	
> datsel <- datsel[diffGenes.f, ]
> pamcl <- pamClassify(datsel, signature, pam.rslt, thresh, postRth=1)
> figClassify(AMC_CRC_clinical, pamcl$pred, pamcl$clu.pred, pamcl$sdat.sig, 
+ pamcl$gclu.f, pamcl$nam.ord)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>