calculate_accuracy: Accuracy calculation of classification method

In a-thind/PathAnalyser: ER & HER2 Pathway Activity Analysis For Breast Cancer Transcriptomic Datasets

Accuracy calculation of classification method

Description

This method provides several classification evaluation metrics to assess the accuracy of predicted pathway classification. The accuracy calculation is performed using predicted pathway activity labels from the employed classification method for each sample and the corresponding true activity labels for the given pathway. A confusion matrix is created to display the classification accuracy decomposed into the distinct pathway activity classes in tabular form for the user. Additional classification evaluation statistics (such as sensitivity, specificity, recall, percentage of classified samples etc) is the optional feature that the user can specify.

Usage

calculate_accuracy(true_labels, predicted_labels, pathway, show_stats = FALSE)

Arguments

true_labels	a data frame, matrix or file name which contains a column named "sample" that consists of sample names / IDs and another column named after a specific pathway which contains the corresponding true pathway activity labels.
predicted_labels	a predicted labels data frame or matrix generated by the classification method yielding predicted pathway activity labels in a column called "class" for the samples in the "sample" column.
pathway	name of pathway used for classification (Note: this pathway name must be present in the true labels data frame / matrix / file name for classification evaluation and generation of the confusion matrix.)
show_stats	an optional flag to display additional statistical information using the confusion matrix and other classification evaluation metrics including: sensitivity, specificity, precision, false positive rate, false negative rate etc.

Value

confusion_matrix

Author(s)

Ozlem Karadeniz [e-mail]

Examples

## Not run: calculate_accuracy(true_labels_df, predicted_labels_df, "ER",
show_stats= TRUE)
## End(Not run)

a-thind/PathAnalyser documentation built on May 6, 2022, 9:50 a.m.