PAM Classification

This function applies classification using Prediction Analysis for Microarrays (PAM) on the provided input object. It supports threshold optimization using cross-validation or the use of all genes without thresholding.

Usage

classification.pam(object, threshold_method = "cv", vt.k = NULL, kfold = 5)

Arguments

object

A precision object containing harmonized data. Must contain the slots harmon.train.data with harmonized training data and harmon.test1.data and harmon.test2.data with harmonized test data.

threshold_method

A character string specifying the thresholding method. Options are: - "cv": Use cross-validation to optimize the threshold. - "none": Use all genes without applying a threshold.

vt.k

A numeric vector of threshold values to evaluate during cross-validation. Only used if threshold_method = "cv".

kfold

An integer specifying the number of folds for cross-validation.

Value

The input object updated with PAM classification results added to the classification.result slot, including predicted classes and associated metrics.