classSNitch: Package for the autonomous classification of RNA structure...
In cbtolson/classSNitch: Classifies RNA Structure Change in Chemical Mapping Data

Description Author(s) References See Also Examples

Package for the autonomous classification of RNA structure change.

Chanin Tolson

A. Liaw and M. Wiener (2002). Classification and Regression by randomForest. R News 2(3), 18–22 (randomForest package)

RNA Mapping Database

getFeatures classifyRNA

#get change features
library("ROCR")
library("gplots")

data("shape_ex")
sample = getFeatures(shape_ex[2:nrow(shape_ex),], base=shape_ex[1,], trim=5)

#predict change
data("mutmap")
cr = classifyRNA(mutmap)
cr_pred = predict(cr, sample, resp="response")

#plot ROC curve (no change v. local/global change)
data("mutmap")
predobj = prediction(cr$votes[,1], mutmap[,1]==1)
perfobj = performance(predobj, 'tpr', 'fpr')
aucobj = performance(predobj, 'auc')
plot(perfobj@x.values[[1]], perfobj@y.values[[1]], lwd=2, 
     type="l", xlab="Specificity", ylab="Sensitivity")
points(c(-1,2),c(-1,2), col="red", type="l")
text(0.8, 0.2, paste("AUC: ", format(aucobj@y.values, digits=2), sep=""), cex=1)