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Wrapper for deprecated OmicSelector_iteratedRFE

Source: R/deprecated.R
OmicSelector_iteratedRFE_deprecated.Rd

This function is DEPRECATED due to data leakage when testSet is provided. The test set labels are used during feature selection, which inflates performance estimates by 10-30

Usage

OmicSelector_iteratedRFE_deprecated(trainSet, testSet = NULL, ...)

Arguments

trainSet

Training data

testSet

Test data (CAUSES LEAKAGE if provided)

...

Other arguments

Value

Original function result with warning

Details

## Why is this deprecated?

The original implementation uses `testSet` during RFE iteration: “` rfeIter(testX = testSet[, initFeatures], testY = testSet[, classLab], ...) “`

This means the model can "see" test data labels during training, leading to overly optimistic accuracy estimates.

## Replacement

Use `OmicPipeline$create_graph_learner()` with nested cross-validation: “` pipeline <- OmicPipeline$new(data, target = "outcome") learner <- pipeline$create_graph_learner(filter = "anova", model = "ranger") service <- BenchmarkService$new(pipeline, outer_folds = 5, inner_folds = 3) service$add_learner(learner) result <- service$run() “`

See also

[OmicPipeline], [BenchmarkService]