# Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion

## Documentation for package ‘DeSousa2013’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

AMC_CRC_clinical | Data used in the package DeSousa2013
AMC_sample_head | Data used in the package DeSousa2013
buildClassifier | Build a gene expression based classifier
cents | Data used in the package DeSousa2013
clu.pred | Data used in the package DeSousa2013
clus | Data used in the package DeSousa2013
clus.f | Data used in the package DeSousa2013
compGapStats | Computing Gap statistics to identify the optimal number of subtypes
conClust | Consensus clustering
CRCPipeLine | Pipeline function for De Sousa 2013
data4surv | Data used in the package DeSousa2013
DeSousa2013 | Pipeline function for De Sousa 2013
diffGenes | Data used in the package DeSousa2013
diffGenes.f | Data used in the package DeSousa2013
err | Data used in the package DeSousa2013
figClassify | Classifying the AMC samples
figGAP | Computing Gap statistics to identify the optimal number of subtypes
figKM | Prognosis of the three subtypes in the AMC data set
figPAMCV | Build a gene expression based classifier
figSilh | Filter colon cancer samples by Silhouette width
filterDiffGenes | Select the most predictive genes from differential genes
filterSamples | Filter colon cancer samples by Silhouette width
findDiffGenes | Search for differential genes between subtypes
gapsmat | Data used in the package DeSousa2013
gapsSE | Data used in the package DeSousa2013
gclu.f | Data used in the package DeSousa2013
ge.all | Data used in the package DeSousa2013
geneExpPre | Preprocessing of the AMC-AJCCII-90 microarray data
getCentroids | Retrieve centroids of a PAM classifier
nam.ord | Data used in the package DeSousa2013
pam.rslt | Data used in the package DeSousa2013
pamClassify | Classifying the AMC samples
pbs2unigenes | Generate a mapping file between probesets and unique gene symbols
pred | Data used in the package DeSousa2013
progAMC | Prognosis of the three subtypes in the AMC data set
sdat | Data used in the package DeSousa2013
sdat.f | Data used in the package DeSousa2013
sdat.sig | Data used in the package DeSousa2013
selPbs | Data used in the package DeSousa2013
selTopVarGenes | Select top variable probesets
signature | Data used in the package DeSousa2013
silh | Data used in the package DeSousa2013
surv | Data used in the package DeSousa2013
survstats | Data used in the package DeSousa2013
thresh | Data used in the package DeSousa2013
uniGenes | Data used in the package DeSousa2013