CNS: Central Nervous System (CNS) cancer data set.

In stepwiseCM: Stepwise Classification of Cancer Samples using High-dimensional Data Sets

Description

A list object includes the measurement of the gene expression in 7128 genes and 60 samples and the clinical risk factors which are Chang stage (nominal), sex (binary), age (nominal), chemo Cx (binary), chemo VP (binary). 21 patients died (labeled 0) and 39 patients survived (labeled 1) within 24 months after the treatment.

References

Pomeroy, SL. and Tamayo, P. and Gaasenbeek, M. and Sturla, LM. and Angelo, M. and McLaughlin, ME. and Kim, JY. and Goumnerova, LC. and Black, PM. and Lau, C. and Allen, JC. and Zagzag, D. and Olson, JM. and Curran, T. and Wetmore, C. and Biegel, JA. and Poggio, T. and Mukherjee, S. and Rifkin, R. and Califano, A. and Stolovitzky, G. and Louis, DN. and Mesirov, JP. and Lander, ES. and Golub, TR. Prediction of Central Nervous System Embryonal Tumour Outcome Based on Gene Expression. Nature., 415(6870):436-442.

Examples

data(CNS)
names(CNS)

Example output

Loading required package: randomForest
randomForest 4.6-12
Type rfNews() to see new features/changes/bug fixes.
Loading required package: MAclinical
Loading required package: party
Loading required package: grid
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Loading required package: strucchange
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: plsgenomics
For any news related to the 'plsgenomics' package (update, corrected bugs), please check http://thoth.inrialpes.fr/people/gdurif/
C++ based sparse PLS routines will soon be available on the CRAN in the new 'fastPLS' package.
Loading required package: st
Loading required package: sda
Loading required package: entropy
Loading required package: corpcor
Loading required package: fdrtool
Loading required package: e1071
Loading required package: tspair
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:randomForest':

    combine

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: pamr
Loading required package: cluster
Loading required package: survival
Loading required package: snowfall
Loading required package: snow

Attaching package: 'snow'

The following objects are masked from 'package:BiocGenerics':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, parApply, parCapply,
    parLapply, parRapply, parSapply

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
    parCapply, parLapply, parRapply, parSapply, splitIndices,
    stopCluster

Loading required package: glmpath
Loading required package: penalized
Welcome to penalized. For extended examples, see vignette("penalized").
[1] "mrna"      "cli"       "class"     "gene.name"

stepwiseCM documentation built on May 31, 2017, 11:47 a.m.