iC10 (version 2.0.2)

goodnessOfFit: Goodness of fit results of the iC10 classifier

Description

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

Usage

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

Value

It prints the correlation for each iC10.

Arguments

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)

Author

Oscar M Rueda

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.

See Also

iC10

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)
goodnessOfFit(res, newdata=features)