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


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Documentation for package ‘DeSousa2013’ version 0.99.3

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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