sig.endoPredict: Signature used to compute the endoPredict signature as...

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

Description

List of 11 genes included in the endoPredict signature. The EntrezGene.ID allows for mapping and the mapping to affy probes is already provided.

Usage

data(sig.endoPredict)

Format

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

References

Filipits, M., Rudas, M., Jakesz, R., Dubsky, P., Fitzal, F., Singer, C. F., et al. (2011). "A new molecular predictor of distant recurrence in ER-positive, HER2-negative breast cancer adds independent information to conventional clinical risk factors." Clinical Cancer Research, 17(18):6012–6020.

Examples

data(sig.endoPredict)
head(sig.endoPredict)

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")'.

      symbol  probe.affy EntrezGene.ID group weight    a    b
BIRC5  BIRC5 202095_s_at           332   GOI   0.41 0.94 -3.8
RBBP8  RBBP8 203344_s_at          5932   GOI  -0.35 0.71 -0.9
UBE2C  UBE2C   202954_at         11065   GOI   0.39 0.79 -1.4
IL6ST  IL6ST   212196_at          3572   GOI  -0.31 0.81 -5.0
AZGP1  AZGP1   209309_at           563   GOI  -0.26 0.67 -0.8
DHCR7  DHCR7 201791_s_at          1717   GOI   0.39 0.89 -4.4

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