ssp2006: SSP2006 classifier for identification of breast cancer...
In genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

Description Usage Format Details Source References Examples

List of parameters defining the SSP2006 classifier for identification of breast cancer molecular subtypes (Hu et al 2006).

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data(ssp2006)
data(ssp2006.scale)
data(ssp2006.robust)

List of parameters for SSP2006:

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.

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:

ssp2006: Use of the official centroids without scaling of the gene expressions.
ssp2006.scale: Use of the official centroids with traditional scaling of the gene expressions (see scale).
ssp2006.robust: Use of the official centroids with robust scaling of the gene expressions (see rescale).

The model ssp2006.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).

http://www.biomedcentral.com/1471-2164/7/96

Hu, Zhiyuan and Fan, Cheng and Oh, Daniel and Marron, JS and He, Xiaping and Qaqish, Bahjat and Livasy, Chad and Carey, Lisa and Reynolds, Evangeline and Dressler, Lynn and Nobel, Andrew and Parker, Joel and Ewend, Matthew and Sawyer, Lynda and Wu, Junyuan and Liu, Yudong and Nanda, Rita and Tretiakova, Maria and Orrico, Alejandra and Dreher, Donna and Palazzo, Juan and Perreard, Laurent and Nelson, Edward and Mone, Mary and Hansen, Heidi and Mullins, Michael and Quackenbush, John and Ellis, Matthew and Olopade, Olufunmilayo and Bernard, Philip and Perou, Charles (2006) "The molecular portraits of breast tumors are conserved across microarray platforms", BMC Genomics, 7(96)

data(ssp2006)
str(ssp2006)
data(ssp2006.robust)
str(ssp2006.robust)

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
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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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

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List of 7
 $ method.cor      : chr "spearman"
 $ method.centroids: chr "mean"
 $ std             : chr "none"
 $ rescale.q       : num 0.05
 $ mins            : num 5
 $ centroids       : num [1:306, 1:5] 2.23 1.363 -0.171 0.317 -0.178 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:306] "AGI_HUM1_OLIGO_A_23_P52761" "AGI_HUM1_OLIGO_A_23_P117882" "AGI_HUM1_OLIGO_A_23_P252832" "AGI_HUM1_OLIGO_A_23_P157371" ...
  .. ..$ : chr [1:5] "Basal" "Her2" "LumA" "LumB" ...
 $ centroids.map   :'data.frame':	306 obs. of  3 variables:
  ..$ probe          : chr [1:306] "AGI_HUM1_OLIGO_A_23_P52761" "AGI_HUM1_OLIGO_A_23_P117882" "AGI_HUM1_OLIGO_A_23_P252832" "AGI_HUM1_OLIGO_A_23_P157371" ...
  ..$ probe.centroids: chr [1:306] "AGI_HUM1_OLIGO_A_23_P52761" "AGI_HUM1_OLIGO_A_23_P117882" "AGI_HUM1_OLIGO_A_23_P252832" "AGI_HUM1_OLIGO_A_23_P157371" ...
  ..$ EntrezGene.ID  : int [1:306] 4316 NA NA NA 9530 5799 NA 23532 9338 1047 ...
List of 7
 $ method.cor      : chr "spearman"
 $ method.centroids: chr "mean"
 $ std             : chr "robust"
 $ rescale.q       : num 0.05
 $ mins            : num 5
 $ centroids       : num [1:306, 1:5] 2.23 1.363 -0.171 0.317 -0.178 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:306] "AGI_HUM1_OLIGO_A_23_P52761" "AGI_HUM1_OLIGO_A_23_P117882" "AGI_HUM1_OLIGO_A_23_P252832" "AGI_HUM1_OLIGO_A_23_P157371" ...
  .. ..$ : chr [1:5] "Basal" "Her2" "LumA" "LumB" ...
 $ centroids.map   :'data.frame':	306 obs. of  3 variables:
  ..$ probe          : chr [1:306] "AGI_HUM1_OLIGO_A_23_P52761" "AGI_HUM1_OLIGO_A_23_P117882" "AGI_HUM1_OLIGO_A_23_P252832" "AGI_HUM1_OLIGO_A_23_P157371" ...
  ..$ probe.centroids: chr [1:306] "AGI_HUM1_OLIGO_A_23_P52761" "AGI_HUM1_OLIGO_A_23_P117882" "AGI_HUM1_OLIGO_A_23_P252832" "AGI_HUM1_OLIGO_A_23_P157371" ...
  ..$ EntrezGene.ID  : int [1:306] 4316 NA NA NA 9530 5799 NA 23532 9338 1047 ...