scmod2.robust: Subtype Clustering Model using ESR1, ERBB2 and AURKA modules...

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

Description

List of parameters defining the Subtype Clustering Model as published in Wirapati et al 2008.

Usage

data(scmod2.robust)

Format

List of parameters for SCMOD2:

parameters

List of parameters for the mixture of three Gaussians (ER-/HER2-, HER2+ and ER+/HER2-) that define the Subtype Clustering Model. The structure is the same than for an Mclust object.

cutoff.AURKA

Cutoff for AURKA module score in order to identify ER+/HER2- High Proliferation (aka Luminal B) tumors and ER+/HER2- Low Proliferation (aka Luminal A) tumors.

mod

ESR1, ERBB2 and AURKA modules.

Source

http://breast-cancer-research.com/content/10/4/R65

References

Wirapati P, Sotiriou C, Kunkel S, Farmer P, Pradervand S, Haibe-Kains B, Desmedt C, Ignatiadis M, Sengstag T, Schutz F, Goldstein DR, Piccart MJ and Delorenzi M (2008) "Meta-analysis of Gene-Expression Profiles in Breast Cancer: Toward a Unified Understanding of Breast Cancer Sub-typing and Prognosis Signatures", Breast Cancer Research, 10(4):R65.

Examples

data(scmod2.robust)
str(scmod2.robust, max.level=1)

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")'.

List of 4
 $ parameters    :List of 3
 $ gaussian.AURKA: Named num [1:2] -0.214 0.192
  ..- attr(*, "names")= chr [1:2] "mean" "sigma"
 $ rescale.q     : num 0.05
 $ mod           :List of 3

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