goodnessOfFit: Goodness of fit results of the iC10 classifier
In iC10: A Copy Number and Expression-Based Classifier for Breast Tumours

Description Usage Arguments Value Author(s) References See Also Examples

Goodness of fit results of the iC10 classifier: this function computes correlations between the signatures of the training dataset and the classified features.

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goodnessOfFit(obj, iC10=1:10, newdata=NULL,...)
## S3 method for class 'iC10'
goodnessOfFit(obj, iC10=1:10, newdata=NULL,...)

`obj`	An object of `iC10` class.
`iC10`	Groups to compute goodness of fit.
`newdata`	The feature data to compute the goodness of fit. Must be the samples classified in `obj`. It can be a call to `matchFeatures` or `normalizeFeatures`. If NULL, `obj$fitted` is used.
`...`	Additional arguments passed to `cor` (like `method`; Default is pearson)

It prints the correlation for each iC10.

Oscar M Rueda

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.

iC10

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