CCM-package {CCM}

Correlation classification method (CCM)

Description

Classification method that classifies an observation based on its correlation with observations having known class labels. There are two main functions. The function create.CCM creates a correlation matrix of correlations between training and test samples. Both Pearson's and Spearman's rank-based correlations are supported. The function predict.CCM assigns class labels to test observations according to the class that has the highest mean correlation by default. However, any (user-defined) function in addition to the mean (e.g., median, max) can be specified.

For a complete list of functions, use 'library(help="CCM")'

Details

Package:	CCM
Type:	Package
Version:	1.2
Date:	2018-04-05
License:	GPL(>=2)
LazyLoad:	yes

Author(s)

Garrett M. Dancik and Yuanbin Ru
Maintainer: Garrett M. Dancik <[e-mail]>

See Also

create.CCM; predict.CCM; plot.CCM

Examples

     ## load data ##
     data(data.expr)
     data(data.gender)

     ## check within class correlations ##
     ## outliers may be caused by poor quality ##
     ## observations or may indicate CCM is not appropriate ##
     K = cor.by.class(data.expr, data.gender)
     ## visualize the results ##
     boxplot(K, xlab = "gender")
     
     ## split dataset into training / testing ##
     train.expr = data.expr[,1:20]
     test.expr = data.expr[,21:40]
     train.gender = data.gender[1:20]
     test.gender = data.gender[21:40]
     
     ## CCM using spearman correlation ##
     K = create.CCM(test.expr, train.expr, method = "spearman")

     ## predict based on the class with the highest mean correlation (the default) ##
     p = predict(K, train.gender)
     table(pred = p, true = test.gender) # check accuracy
    
     ## plot correlations for the 3rd observation ##
     plot(K, train.gender, index = 3, main = "correlations for obs #3", 
	       xlab = "gender", ylab = "correlation")