nkis: Gene expression, annotations and clinical data from van de...

In genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

Description

This dataset contains (part of) the gene expression, annotations and clinical data as published in van de Vijver et al. 2002.

Usage

data(nkis)

Format

nkis is a dataset containing three matrices:

data.nkis

Matrix containing gene expressions as measured by Agilent technology (dual-channel, oligonucleotides

annot.nkis

Matrix containing annotations of Agilent microarray platform

demo.nkis

Clinical information of the breast cancer patients whose tumors were hybridized

Details

This dataset represent only partially the one published by van de Vijver et al. in 2008. Indeed, only part of the patients (150) and gene expressions (922) are contained in data.nkis.

Source

http://www.nature.com/nature/journal/v415/n6871/full/415530a.html

References

M. J. van de Vijver and Y. D. He and L. van't Veer and H. Dai and A. M. Hart and D. W. Voskuil and G. J. Schreiber and J. L. Peterse and C. Roberts and M. J. Marton and M. Parrish and D. Atsma and A. Witteveen and A. Glas and L. Delahaye and T. van der Velde and H. Bartelink and S. Rodenhuis and E. T. Rutgers and S. H. Friend and R. Bernards (2002) "A Gene Expression Signature as a Predictor of Survival in Breast Cancer", New England Journal of Medicine, 347(25):1999–2009

Examples

data(nkis)

Example output

Loading required package: survcomp
Loading required package: survival
Loading required package: prodlim
Loading required package: mclust
Package 'mclust' version 5.3
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: limma
Loading required package: biomaRt
Loading required package: iC10
Loading required package: pamr
Loading required package: cluster
Loading required package: iC10TrainingData
Loading required package: AIMS
Loading required package: e1071
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:limma':

    plotMA

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")'.

genefu documentation built on Jan. 28, 2021, 2:01 a.m.