compare: Compare results of the iC10 classifier

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

Description

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

Usage

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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

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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.