compare: Compare results of the iC10 classifier

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

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)

Example output

Loading required package: pamr
Loading required package: cluster
Loading required package: survival
Loading required package: iC10TrainingData
running classifier with only expression...
12345678910111213141516171819202122232425262728293012345678910Fold 1 :123456789101112131415161718192021222324252627282930
Fold 2 :123456789101112131415161718192021222324252627282930
Fold 3 :123456789101112131415161718192021222324252627282930
Fold 4 :123456789101112131415161718192021222324252627282930
Fold 5 :123456789101112131415161718192021222324252627282930
Fold 6 :123456789101112131415161718192021222324252627282930
Fold 7 :123456789101112131415161718192021222324252627282930
Fold 8 :123456789101112131415161718192021222324252627282930
Fold 9 :123456789101112131415161718192021222324252627282930
Fold 10 :123456789101112131415161718192021222324252627282930

iC10 documentation built on May 2, 2019, 6:35 a.m.