compare: Compare results of the iC10 classifier

In iC10: A Copy Number and Expression-Based Classifier for Breast Tumours

Compare results of the iC10 classifier

Description

This function plots the centroids of the training set versus the average profiles of the new data classified in each group.

Usage

compare(obj, iC10=1:10, newdata, name.test="Test",...)
## S3 method for class 'iC10'
compare(obj, iC10=1:10, newdata, name.test="Test",...)

Arguments

obj	An object of class iC10, a result of a call to iC10()
iC10	Groups to plot
newdata	Set of features of the new data to compare. They must be the same samples classified and contained in x. A result of a call to matchFeatures() or normalizeFeatures()
name.test	Name of the new data set to appear in the text of the plot
...	Additional arguments passed to plot()

Value

A plot is returned with two plots per groups requested.

Author(s)

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, plot.iC10, matchFeatures, normalizeFeatures

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)
compare(res, 1:3, newdata=features)

iC10 documentation built on Sept. 11, 2024, 6:22 p.m.