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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | #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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.