Description Usage Arguments Value
Create a "truth" plot, which plots HINT v. Wellington scores given a model and a threshold to use for determining a "positive"
1 | createTruthPlot(model, modelType, seed, threshold, X_test, y_test, plotFile)
|
model |
A model trained on the annotated dataset, either a linear or gradient-boosted model |
modelType |
Either "boosted" or "linear" to indicate the type of model provided |
seed |
One of "16", "20", or "both", denoting which seed is being used |
threshold |
A numeric from 0-1 indicating the cutoff for what constitutes a "positive" probability. This is an INCLUSIVE value; positives are greater than or equal to the threshold |
X_test |
The matrix of test data for predictors, generally created using "prepModelData" |
y_test |
The matrix of test data for response, generally created using "prepModelData" |
plotFile |
A location to use for creating the png plot file |
The "truth data frame", containing the Wellington/HINT scores for each point in the test set, the predicted probability of a ChIPseq hit, the binary prediction based on that probability and the supplied threshold, the true ChIPseq hit value, and the corresponding label of TP/TN/FP/FN.
It also constructs and saves a plot of HINT vs Wellington scores, where both have been transformed via asinh() and the Wellington scores have been converted via absolute value. Points are coded by confusion matrix outcome.
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