reptile_eval_prediction: Evaluating the prediction results

In REPTILE: Regulatory DNA Element Prediction

Description

Function used to evaluate the predictions by comparing enhancer scores from reptile_predict or reptile_predict_genome_wide and the correct labels. Area under the Receiver Operating Characteristic (ROC) curve (AUROC) and Area under the Precision-Recall curve (AUPR) will be calculated.

Usage

reptile_eval_prediction(predictions,annotations)

Arguments

predictions	vector of enhancer scores for regions. The name of each value (score) corresponds to the id of the region.
annotations	vector of labels for regions with the same length as predictions. The name of each value (label) corresponds to the id of the region. Only two values are allowed in annotations: 0 (negative) and 1 (positive). No NA is allowed.

Value

A list containing two numbers

AUROC	Area under the Receiver Operating Characteristic (ROC) curve
AUPR	Area under the Precision-Recall curve

Author(s)

Yupeng He [e-mail]

See Also

reptile_predict, reptile_predict_genome_wide

Examples

library("REPTILE")
data("rsd")

## Training
rsd_model <- reptile_train(rsd$training_data$region_epimark,
                           rsd$training_data$region_label,
                           rsd$training_data$DMR_epimark,
                           rsd$training_data$DMR_label,
                           ntree=50)

## Prediction
## - REPTILE
pred <- reptile_predict(rsd_model,
                        rsd$test_data$region_epimark,
                        rsd$test_data$DMR_epimark)
## - Random guessing
pred_guess = runif(length(pred$D))
names(pred_guess) = names(pred$D)

## Evaluation
res_reptile <- reptile_eval_prediction(pred$D,
                                       rsd$test_data$region_label)
res_guess <- reptile_eval_prediction(pred_guess,
                                     rsd$test_data$region_label)
## - Print AUROC and AUPR
cat(paste0("REPTILE\n",
           "  AUROC = ",round(res_reptile$AUROC,digit=3),
           "\n",
           "  AUPR  = ",round(res_reptile$AUPR,digit=3))
    ,"\n")
cat(paste0("Random guessing\n",
           "  AUROC = ",round(res_guess$AUROC,digit=3),
           "\n",
           "  AUPR  = ",round(res_guess$AUPR,digit=3))
   ,"\n")

REPTILE documentation built on May 2, 2019, 5:06 a.m.