SSP2003 classifier for identification of breast cancer molecular subtypes (Sorlie et al 2003)

Description

List of parameters defining the SSP2003 classifier for identification of breast cancer molecular subtypes (Sorlie et al 2003).

Usage

data(ssp2003)
data(ssp2003.scale)
data(ssp2003.robust)

Format

List of parameters for SSP2003:

centroids

Gene expression centroids for each subtype.

centroids.map

Mapping for centroids.

method.cor

Method of correlation used to compute distance to the centroids.

method.centroids

Method used to compute the centroids.

std

Method of standardization for gene expressions.

mins

Minimum number of samples within each cluster allowed during the fitting of the model.

Details

Three versions of the model are provided, each of ones differs by the gene expressions standardization method since it has an important impact on the subtype classification:

ssp2003

Use of the official centroids without scaling of the gene expressions.

ssp2003.scale

Use of the official centroids with traditional scaling of the gene expressions (see scale).

ssp2003.robust

Use of the official centroids with robust scaling of the gene expressions (see rescale).

The model ssp2003.robust has been shown to reach the best concordance with the traditional clinical parameters (ER IHC, HER2 IHC/FISH and histological grade). However the use of this model is recommended only when the dataset is representative of a global population of breast cancer patients (no sampling bias, the 5 subtypes should be present).

Source

http://www.pnas.org/content/100/14/8418

References

T. Sorlie and R. Tibshirani and J. Parker and T. Hastie and J. S. Marron and A. Nobel and S. Deng and H. Johnsen and R. Pesich and S. Geister and J. Demeter and C. Perou and P. E. Lonning and P. O. Brown and A. L. Borresen-Dale and D. Botstein (2003) "Repeated Observation of Breast Tumor Subtypes in Independent Gene Expression Data Sets", Proceedings of the National Academy of Sciences, 1(14):8418–8423

Examples

data(ssp2003)
str(ssp2003)
data(ssp2003.robust)
str(ssp2003.robust)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(genefu)
Loading required package: survcomp
Loading required package: survival
Loading required package: prodlim
Loading required package: mclust
Package 'mclust' version 5.2
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

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

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/genefu/ssp2003.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ssp2003
> ### Title: SSP2003 classifier for identification of breast cancer molecular
> ###   subtypes (Sorlie et al 2003)
> ### Aliases: ssp2003 ssp2003.scale ssp2003.robust
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(ssp2003)
> str(ssp2003)
List of 7
 $ method.cor      : chr "spearman"
 $ method.centroids: chr "mean"
 $ std             : chr "none"
 $ rescale.q       : num 0.05
 $ mins            : num 5
 $ centroids       : num [1:500, 1:5] -5.04 -3.3 -3.28 -2.63 -2.31 -2.16 -1.95 -1.89 -1.85 -1.84 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:500] "IMAGE:84786" "IMAGE:725321" "IMAGE:298417" "IMAGE:417867" ...
  .. ..$ : chr [1:5] "Basal" "Her2" "LumA" "LumB" ...
 $ centroids.map   :'data.frame':	500 obs. of  3 variables:
  ..$ probe          : chr [1:500] "IMAGE:84786" "IMAGE:725321" "IMAGE:298417" "IMAGE:417867" ...
  ..$ probe.centroids: chr [1:500] "IMAGE:84786" "IMAGE:725321" "IMAGE:298417" "IMAGE:417867" ...
  ..$ EntrezGene.ID  : int [1:500] NA 2099 7033 7494 30061 4680 57758 255743 10451 6337 ...
> data(ssp2003.robust)
> str(ssp2003.robust)
List of 7
 $ method.cor      : chr "spearman"
 $ method.centroids: chr "mean"
 $ std             : chr "robust"
 $ rescale.q       : num 0.05
 $ mins            : num 5
 $ centroids       : num [1:500, 1:5] -5.04 -3.3 -3.28 -2.63 -2.31 -2.16 -1.95 -1.89 -1.85 -1.84 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:500] "IMAGE:84786" "IMAGE:725321" "IMAGE:298417" "IMAGE:417867" ...
  .. ..$ : chr [1:5] "Basal" "Her2" "LumA" "LumB" ...
 $ centroids.map   :'data.frame':	500 obs. of  3 variables:
  ..$ probe          : chr [1:500] "IMAGE:84786" "IMAGE:725321" "IMAGE:298417" "IMAGE:417867" ...
  ..$ probe.centroids: chr [1:500] "IMAGE:84786" "IMAGE:725321" "IMAGE:298417" "IMAGE:417867" ...
  ..$ EntrezGene.ID  : int [1:500] NA 2099 7033 7494 30061 4680 57758 255743 10451 6337 ...
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>