sig.oncotypedx: Signature used to compute the OncotypeDX signature as...

Description Usage Format References Examples


List of 21 genes included in the OncotypeDX signature. The EntrezGene.ID allows for mapping and the mapping to affy probes is already provided.




sig.oncotypedx is a matrix with 5 columns containing the annotations and information related to the signature itself (including a mapping to Affymetrix HGU platform).


S. Paik, S. Shak, G. Tang, C. Kim, J. Bakker, M. Cronin, F. L. Baehner, M. G. Walker, D. Watson, T. Park, W. Hiller, E. R. Fisher, D. L. Wickerham, J. Bryant, and N. Wolmark (2004) "A Multigene Assay to Predict Recurrence of Tamoxifen-Treated, Node-Negative Breast Cancer", New England Journal of Medicine, 351(27):2817–2826.



Example output

Loading required package: survcomp
Loading required package: survival
Loading required package: prodlim
Loading required package: mclust
Package 'mclust' version 5.4.3
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: impute
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':


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,, basename, cbind, colMeans, colSums, colnames,
    dirname,, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax,, pmin,, 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")'.

      symbol  probe.affy EntrezGene.ID         group weight
MKI67  MKI67 212022_s_at          4288 proliferation  0.208
AURKA  AURKA 208079_s_at          6790 proliferation  0.208
BIRC5  BIRC5 202095_s_at           332 proliferation  0.208
CCNB1  CCNB1 214710_s_at           891 proliferation  0.208
MYBL2  MYBL2   201710_at          4605 proliferation  0.208
MMP11  MMP11 203876_s_at          4320      invasion  0.050

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