iC10-package {iC10}

A Copy Number and Expression-Based Classifier for Breast Tumours

Description

Implementation of the classifier described in the paper Ali HR et al (2014) <doi:10.1186/s13059-014-0431-1>. It uses copy number and/or expression form breast cancer data, trains a Tibshirani's 'pamr' classifier with the features available and predicts the iC10 group.

Details

The DESCRIPTION file:

Package:	iC10
Type:	Package
Title:	A Copy Number and Expression-Based Classifier for Breast Tumours
Version:	2.0.2
Date:	2024-07-16
Authors@R:	person("Oscar M", "Rueda", , "[e-mail]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0008-4884"))
Maintainer:	Oscar M Rueda <[e-mail]>
Description:	Implementation of the classifier described in the paper Ali HR et al (2014) <doi:10.1186/s13059-014-0431-1>. It uses copy number and/or expression form breast cancer data, trains a Tibshirani's 'pamr' classifier with the features available and predicts the iC10 group.
License:	GPL-3
Imports:	pamr, impute, iC10TrainingData
Packaged:	2015-09-23 02:37:41 UTC; rueda01
NeedsCompilation:	no
Repository:	CRAN
Date/Publication:	2015-09-23 08:05:08
Author:	Oscar M Rueda [aut, cre] (<https://orcid.org/0000-0003-0008-4884>)

Index of help topics:

compare                 Compare results of the iC10 classifier
getCNfeatures           Internal function for matching copy number
                        features.
getExpfeatures          Internal function for matching expression
                        features.
goodnessOfFit           Goodness of fit results of the iC10 classifier
iC10                    A copy number and expression-based classfier
                        for breast cancers
iC10-package            A Copy Number and Expression-Based Classifier
                        for Breast Tumours
matchFeatures           Matching features from the classifier to the
                        test data.
normalizeFeatures       Normalization of expression features
plot.iC10               Plot results of the iC10 classifier
print.iC10              Print results of the iC10 classifier
summary.iC10            Summary results of the iC10 classifier

iC10 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.

Author(s)

NA

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

References

Ali HR et al. Genome-driven integrated classification of breast cancer validated in over 7,500 samples. Genome Biology 2014; 15:431. 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.

Examples

require(iC10TrainingData)
data(train.CN)
data(train.Exp)
features <- matchFeatures(Exp=train.Exp, Exp.by.feat="probe")
features <- normalizeFeatures(features, "scale")
res <- iC10(features)
summary(res)
goodnessOfFit(res, newdata=features)
compare(res, iC10=1:2, newdata=features)
compare(res, iC10=2:4, newdata=features)