iC10TrainingData-package {iC10TrainingData}

Training Datasets for iC10 Package

Description

Training datasets for iC10; which implements the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group. Genomic annotation for the training dataset has been obtained from Mark Dunning's lluminaHumanv3.db package. Training datasets for iC10; which implements the classifier described in the METABRIC paper 'The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups' (Curtis et al., Nature 2012). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group.

Details

The DESCRIPTION file:

Package:	iC10TrainingData
Type:	Package
Title:	Training Datasets for iC10 Package
Version:	2.0.1
Date:	2024-07-16
Author:	Oscar M Rueda and Jose Antonio Seoane Fernandez
Maintainer:	Oscar M. Rueda <[e-mail]>
Description:	Training datasets for iC10; which implements the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group. Genomic annotation for the training dataset has been obtained from Mark Dunning's lluminaHumanv3.db package.
License:	GPL-3
Packaged:	2014-09-15 12:22:07 UTC; rueda01
NeedsCompilation:	no
Repository:	CRAN
Date/Publication:	2014-09-26 12:13:01

Index of help topics:

IntClustMemb            Class Membership for the training set
Map.All                 Probe mapping of the complete set of features
                        of the training set
Map.CN                  Probe mapping of the copy number features of
                        the training set.
Map.Exp                 Probe mapping of the Expression features of the
                        training set
iC10TrainingData-package
                        Training Datasets for iC10 Package
train.CN                Copy number data for the training set
train.Exp               Expression data for the training set.

Training datasets for iC10; which implements the classifier described in the METABRIC paper 'The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups' (Curtis et al., Nature 2012). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group.

Author(s)

Oscar M Rueda and Jose Antonio Seoane Fernandez

Maintainer: Oscar M. Rueda <[e-mail]>

References

Curtis et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 2012; 486:346-352. Tibshirani et al. Diagnosis of multiple cancer types by shrunken centroids of gene expression. PNAS 2002; 99(10):6567-6572.

See Also

iC10

Examples

data(train.CN)
data(train.Exp)