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<!DOCTYPE html>
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<title>Section 1 Melanin binding pilot peptide array | Multifunctional peptide engineering</title>
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<meta name="author" content="Renee Ti Chou and Henry T. Hsueh" />
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<ul class="summary">
<li><a href="./"><i>Multifunctional peptide engineering</i></a></li>
<li class="divider"></li>
<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Preface</a></li>
<li class="chapter" data-level="1" data-path="id_01_pilot_peptide_array.html"><a href="id_01_pilot_peptide_array.html"><i class="fa fa-check"></i><b>1</b> Melanin binding pilot peptide array</a>
<ul>
<li class="chapter" data-level="1.1" data-path="id_01_pilot_peptide_array.html"><a href="id_01_pilot_peptide_array.html#overview"><i class="fa fa-check"></i><b>1.1</b> Overview</a></li>
<li class="chapter" data-level="1.2" data-path="id_01_pilot_peptide_array.html"><a href="id_01_pilot_peptide_array.html#generating-ml-input"><i class="fa fa-check"></i><b>1.2</b> Generating ML input</a></li>
<li class="chapter" data-level="1.3" data-path="id_01_pilot_peptide_array.html"><a href="id_01_pilot_peptide_array.html#training-initial-rf-model"><i class="fa fa-check"></i><b>1.3</b> Training initial RF model</a></li>
<li class="chapter" data-level="1.4" data-path="id_01_pilot_peptide_array.html"><a href="id_01_pilot_peptide_array.html#melanin-binding-variable-importance"><i class="fa fa-check"></i><b>1.4</b> Melanin binding variable importance</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html"><i class="fa fa-check"></i><b>2</b> Variable reduction</a>
<ul>
<li class="chapter" data-level="2.1" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#methods"><i class="fa fa-check"></i><b>2.1</b> Methods</a>
<ul>
<li class="chapter" data-level="2.1.1" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#regression"><i class="fa fa-check"></i><b>2.1.1</b> Regression</a></li>
<li class="chapter" data-level="2.1.2" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#classification"><i class="fa fa-check"></i><b>2.1.2</b> Classification</a>
<ul>
<li class="chapter" data-level="2.1.2.1" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#extension-to-multi-class-classification"><i class="fa fa-check"></i><b>2.1.2.1</b> Extension to multi-class classification</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="2.2" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#ml-input-generating-function"><i class="fa fa-check"></i><b>2.2</b> ML input generating function</a></li>
<li class="chapter" data-level="2.3" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#aic-functions"><i class="fa fa-check"></i><b>2.3</b> AIC functions</a></li>
<li class="chapter" data-level="2.4" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#melanin-binding-regression"><i class="fa fa-check"></i><b>2.4</b> Melanin binding (regression)</a>
<ul>
<li class="chapter" data-level="2.4.1" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#generating-ml-input-1"><i class="fa fa-check"></i><b>2.4.1</b> Generating ML input</a></li>
<li class="chapter" data-level="2.4.2" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#variable-importance"><i class="fa fa-check"></i><b>2.4.2</b> Variable importance</a></li>
<li class="chapter" data-level="2.4.3" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#variable-reduction"><i class="fa fa-check"></i><b>2.4.3</b> Variable reduction</a></li>
<li class="chapter" data-level="2.4.4" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#generating-train-test-splits"><i class="fa fa-check"></i><b>2.4.4</b> Generating train-test splits</a></li>
</ul></li>
<li class="chapter" data-level="2.5" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#cell-penetration-classification"><i class="fa fa-check"></i><b>2.5</b> Cell-penetration (classification)</a>
<ul>
<li class="chapter" data-level="2.5.1" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#generating-ml-input-2"><i class="fa fa-check"></i><b>2.5.1</b> Generating ML input</a></li>
<li class="chapter" data-level="2.5.2" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#variable-importance-1"><i class="fa fa-check"></i><b>2.5.2</b> Variable importance</a></li>
<li class="chapter" data-level="2.5.3" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#variable-reduction-1"><i class="fa fa-check"></i><b>2.5.3</b> Variable reduction</a></li>
<li class="chapter" data-level="2.5.4" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#generating-train-test-splits-1"><i class="fa fa-check"></i><b>2.5.4</b> Generating train-test splits</a></li>
</ul></li>
<li class="chapter" data-level="2.6" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#toxicity-classification"><i class="fa fa-check"></i><b>2.6</b> Toxicity (classification)</a>
<ul>
<li class="chapter" data-level="2.6.1" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#generating-ml-input-3"><i class="fa fa-check"></i><b>2.6.1</b> Generating ML input</a></li>
<li class="chapter" data-level="2.6.2" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#variable-importance-2"><i class="fa fa-check"></i><b>2.6.2</b> Variable importance</a></li>
<li class="chapter" data-level="2.6.3" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#variable-reduction-2"><i class="fa fa-check"></i><b>2.6.3</b> Variable reduction</a></li>
<li class="chapter" data-level="2.6.4" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#generating-train-test-splits-2"><i class="fa fa-check"></i><b>2.6.4</b> Generating train-test splits</a></li>
</ul></li>
<li class="chapter" data-level="2.7" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#plotting"><i class="fa fa-check"></i><b>2.7</b> Plotting</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="id_03_model_training.html"><a href="id_03_model_training.html"><i class="fa fa-check"></i><b>3</b> Model training</a>
<ul>
<li class="chapter" data-level="3.1" data-path="id_03_model_training.html"><a href="id_03_model_training.html#overview-1"><i class="fa fa-check"></i><b>3.1</b> Overview</a></li>
<li class="chapter" data-level="3.2" data-path="id_03_model_training.html"><a href="id_03_model_training.html#general-codefunctions"><i class="fa fa-check"></i><b>3.2</b> General code/functions</a></li>
<li class="chapter" data-level="3.3" data-path="id_03_model_training.html"><a href="id_03_model_training.html#melanin-binding-regression-1"><i class="fa fa-check"></i><b>3.3</b> Melanin binding (regression)</a>
<ul>
<li class="chapter" data-level="3.3.1" data-path="id_03_model_training.html"><a href="id_03_model_training.html#model-training"><i class="fa fa-check"></i><b>3.3.1</b> Model training</a></li>
<li class="chapter" data-level="3.3.2" data-path="id_03_model_training.html"><a href="id_03_model_training.html#inner-cross-validation"><i class="fa fa-check"></i><b>3.3.2</b> Inner cross-validation</a></li>
<li class="chapter" data-level="3.3.3" data-path="id_03_model_training.html"><a href="id_03_model_training.html#training-on-whole-data-set"><i class="fa fa-check"></i><b>3.3.3</b> Training on whole data set</a></li>
<li class="chapter" data-level="3.3.4" data-path="id_03_model_training.html"><a href="id_03_model_training.html#model-evaluation"><i class="fa fa-check"></i><b>3.3.4</b> Model evaluation</a></li>
<li class="chapter" data-level="3.3.5" data-path="id_03_model_training.html"><a href="id_03_model_training.html#inner-loop-model-selection"><i class="fa fa-check"></i><b>3.3.5</b> Inner loop model selection</a>
<ul>
<li class="chapter" data-level="3.3.5.1" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-1"><i class="fa fa-check"></i><b>3.3.5.1</b> CV 1</a></li>
<li class="chapter" data-level="3.3.5.2" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-2"><i class="fa fa-check"></i><b>3.3.5.2</b> CV 2</a></li>
<li class="chapter" data-level="3.3.5.3" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-3"><i class="fa fa-check"></i><b>3.3.5.3</b> CV 3</a></li>
<li class="chapter" data-level="3.3.5.4" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-4"><i class="fa fa-check"></i><b>3.3.5.4</b> CV 4</a></li>
<li class="chapter" data-level="3.3.5.5" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-5"><i class="fa fa-check"></i><b>3.3.5.5</b> CV 5</a></li>
<li class="chapter" data-level="3.3.5.6" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-6"><i class="fa fa-check"></i><b>3.3.5.6</b> CV 6</a></li>
<li class="chapter" data-level="3.3.5.7" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-7"><i class="fa fa-check"></i><b>3.3.5.7</b> CV 7</a></li>
<li class="chapter" data-level="3.3.5.8" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-8"><i class="fa fa-check"></i><b>3.3.5.8</b> CV 8</a></li>
<li class="chapter" data-level="3.3.5.9" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-9"><i class="fa fa-check"></i><b>3.3.5.9</b> CV 9</a></li>
<li class="chapter" data-level="3.3.5.10" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-10"><i class="fa fa-check"></i><b>3.3.5.10</b> CV 10</a></li>
</ul></li>
<li class="chapter" data-level="3.3.6" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-evaluation"><i class="fa fa-check"></i><b>3.3.6</b> Final evaluation</a></li>
<li class="chapter" data-level="3.3.7" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-model-selection"><i class="fa fa-check"></i><b>3.3.7</b> Final model selection</a></li>
<li class="chapter" data-level="3.3.8" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-reduced-sl"><i class="fa fa-check"></i><b>3.3.8</b> Final reduced SL</a></li>
</ul></li>
<li class="chapter" data-level="3.4" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cell-penetration-classification-1"><i class="fa fa-check"></i><b>3.4</b> Cell-penetration (classification)</a>
<ul>
<li class="chapter" data-level="3.4.1" data-path="id_03_model_training.html"><a href="id_03_model_training.html#model-training-1"><i class="fa fa-check"></i><b>3.4.1</b> Model training</a></li>
<li class="chapter" data-level="3.4.2" data-path="id_03_model_training.html"><a href="id_03_model_training.html#inner-cross-validation-1"><i class="fa fa-check"></i><b>3.4.2</b> Inner cross-validation</a></li>
<li class="chapter" data-level="3.4.3" data-path="id_03_model_training.html"><a href="id_03_model_training.html#training-on-whole-data-set-1"><i class="fa fa-check"></i><b>3.4.3</b> Training on whole data set</a></li>
<li class="chapter" data-level="3.4.4" data-path="id_03_model_training.html"><a href="id_03_model_training.html#model-evaluation-1"><i class="fa fa-check"></i><b>3.4.4</b> Model evaluation</a></li>
<li class="chapter" data-level="3.4.5" data-path="id_03_model_training.html"><a href="id_03_model_training.html#inner-loop-model-selection-1"><i class="fa fa-check"></i><b>3.4.5</b> Inner loop model selection</a>
<ul>
<li class="chapter" data-level="3.4.5.1" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-1-1"><i class="fa fa-check"></i><b>3.4.5.1</b> CV 1</a></li>
<li class="chapter" data-level="3.4.5.2" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-2-1"><i class="fa fa-check"></i><b>3.4.5.2</b> CV 2</a></li>
<li class="chapter" data-level="3.4.5.3" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-3-1"><i class="fa fa-check"></i><b>3.4.5.3</b> CV 3</a></li>
<li class="chapter" data-level="3.4.5.4" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-4-1"><i class="fa fa-check"></i><b>3.4.5.4</b> CV 4</a></li>
<li class="chapter" data-level="3.4.5.5" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-5-1"><i class="fa fa-check"></i><b>3.4.5.5</b> CV 5</a></li>
<li class="chapter" data-level="3.4.5.6" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-6-1"><i class="fa fa-check"></i><b>3.4.5.6</b> CV 6</a></li>
<li class="chapter" data-level="3.4.5.7" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-7-1"><i class="fa fa-check"></i><b>3.4.5.7</b> CV 7</a></li>
<li class="chapter" data-level="3.4.5.8" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-8-1"><i class="fa fa-check"></i><b>3.4.5.8</b> CV 8</a></li>
<li class="chapter" data-level="3.4.5.9" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-9-1"><i class="fa fa-check"></i><b>3.4.5.9</b> CV 9</a></li>
<li class="chapter" data-level="3.4.5.10" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-10-1"><i class="fa fa-check"></i><b>3.4.5.10</b> CV 10</a></li>
</ul></li>
<li class="chapter" data-level="3.4.6" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-evaluation-1"><i class="fa fa-check"></i><b>3.4.6</b> Final evaluation</a></li>
<li class="chapter" data-level="3.4.7" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-model-selection-1"><i class="fa fa-check"></i><b>3.4.7</b> Final model selection</a></li>
<li class="chapter" data-level="3.4.8" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-reduced-sl-1"><i class="fa fa-check"></i><b>3.4.8</b> Final reduced SL</a></li>
</ul></li>
<li class="chapter" data-level="3.5" data-path="id_03_model_training.html"><a href="id_03_model_training.html#toxicity-classification-1"><i class="fa fa-check"></i><b>3.5</b> Toxicity (classification)</a>
<ul>
<li class="chapter" data-level="3.5.1" data-path="id_03_model_training.html"><a href="id_03_model_training.html#model-training-2"><i class="fa fa-check"></i><b>3.5.1</b> Model training</a></li>
<li class="chapter" data-level="3.5.2" data-path="id_03_model_training.html"><a href="id_03_model_training.html#inner-cross-validation-2"><i class="fa fa-check"></i><b>3.5.2</b> Inner cross-validation</a></li>
<li class="chapter" data-level="3.5.3" data-path="id_03_model_training.html"><a href="id_03_model_training.html#training-on-whole-data-set-2"><i class="fa fa-check"></i><b>3.5.3</b> Training on whole data set</a></li>
<li class="chapter" data-level="3.5.4" data-path="id_03_model_training.html"><a href="id_03_model_training.html#model-evaluation-2"><i class="fa fa-check"></i><b>3.5.4</b> Model evaluation</a></li>
<li class="chapter" data-level="3.5.5" data-path="id_03_model_training.html"><a href="id_03_model_training.html#inner-loop-model-selection-2"><i class="fa fa-check"></i><b>3.5.5</b> Inner loop model selection</a>
<ul>
<li class="chapter" data-level="3.5.5.1" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-1-2"><i class="fa fa-check"></i><b>3.5.5.1</b> CV 1</a></li>
<li class="chapter" data-level="3.5.5.2" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-2-2"><i class="fa fa-check"></i><b>3.5.5.2</b> CV 2</a></li>
<li class="chapter" data-level="3.5.5.3" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-3-2"><i class="fa fa-check"></i><b>3.5.5.3</b> CV 3</a></li>
<li class="chapter" data-level="3.5.5.4" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-4-2"><i class="fa fa-check"></i><b>3.5.5.4</b> CV 4</a></li>
<li class="chapter" data-level="3.5.5.5" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-5-2"><i class="fa fa-check"></i><b>3.5.5.5</b> CV 5</a></li>
<li class="chapter" data-level="3.5.5.6" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-6-2"><i class="fa fa-check"></i><b>3.5.5.6</b> CV 6</a></li>
<li class="chapter" data-level="3.5.5.7" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-7-2"><i class="fa fa-check"></i><b>3.5.5.7</b> CV 7</a></li>
<li class="chapter" data-level="3.5.5.8" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-8-2"><i class="fa fa-check"></i><b>3.5.5.8</b> CV 8</a></li>
<li class="chapter" data-level="3.5.5.9" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-9-2"><i class="fa fa-check"></i><b>3.5.5.9</b> CV 9</a></li>
<li class="chapter" data-level="3.5.5.10" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-10-2"><i class="fa fa-check"></i><b>3.5.5.10</b> CV 10</a></li>
</ul></li>
<li class="chapter" data-level="3.5.6" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-evaluation-2"><i class="fa fa-check"></i><b>3.5.6</b> Final evaluation</a></li>
<li class="chapter" data-level="3.5.7" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-model-selection-2"><i class="fa fa-check"></i><b>3.5.7</b> Final model selection</a></li>
<li class="chapter" data-level="3.5.8" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-reduced-sl-2"><i class="fa fa-check"></i><b>3.5.8</b> Final reduced SL</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="4" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html"><i class="fa fa-check"></i><b>4</b> Model validation and interpretation</a>
<ul>
<li class="chapter" data-level="4.1" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#model-validation"><i class="fa fa-check"></i><b>4.1</b> Model validation</a>
<ul>
<li class="chapter" data-level="4.1.1" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#melaning-binding"><i class="fa fa-check"></i><b>4.1.1</b> Melaning binding</a></li>
<li class="chapter" data-level="4.1.2" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#melanin-binding-and-cell-penetration"><i class="fa fa-check"></i><b>4.1.2</b> Melanin binding and cell-penetration</a></li>
<li class="chapter" data-level="4.1.3" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#melanin-induced-cells"><i class="fa fa-check"></i><b>4.1.3</b> Melanin-induced cells</a></li>
<li class="chapter" data-level="4.1.4" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#non-melanin-induced-cells"><i class="fa fa-check"></i><b>4.1.4</b> Non-melanin induced cells</a></li>
</ul></li>
<li class="chapter" data-level="4.2" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#overall-model-interpretation"><i class="fa fa-check"></i><b>4.2</b> Overall model interpretation</a>
<ul>
<li class="chapter" data-level="4.2.1" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#melanin-binding-regression-2"><i class="fa fa-check"></i><b>4.2.1</b> Melanin binding (regression)</a></li>
<li class="chapter" data-level="4.2.2" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#cell-penetration-classification-2"><i class="fa fa-check"></i><b>4.2.2</b> Cell-penetration (classification)</a></li>
<li class="chapter" data-level="4.2.3" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#toxicity-classification-2"><i class="fa fa-check"></i><b>4.2.3</b> Toxicity (classification)</a></li>
</ul></li>
<li class="chapter" data-level="4.3" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#multifunctional-peptide-selection"><i class="fa fa-check"></i><b>4.3</b> Multifunctional peptide selection</a></li>
<li class="chapter" data-level="4.4" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#explanation-of-hr97-predictions"><i class="fa fa-check"></i><b>4.4</b> Explanation of HR97 predictions</a>
<ul>
<li class="chapter" data-level="4.4.1" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#melanin-binding"><i class="fa fa-check"></i><b>4.4.1</b> Melanin binding</a></li>
<li class="chapter" data-level="4.4.2" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#cell-penetration"><i class="fa fa-check"></i><b>4.4.2</b> Cell-penetration</a></li>
<li class="chapter" data-level="4.4.3" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#toxicity"><i class="fa fa-check"></i><b>4.4.3</b> Toxicity</a></li>
</ul></li>
<li class="chapter" data-level="4.5" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#peptide-design-space-visualization"><i class="fa fa-check"></i><b>4.5</b> Peptide design space visualization</a></li>
</ul></li>
<li class="chapter" data-level="5" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html"><i class="fa fa-check"></i><b>5</b> Adversarial computational control</a>
<ul>
<li class="chapter" data-level="5.1" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#general-codefunctions-1"><i class="fa fa-check"></i><b>5.1</b> General code/functions</a></li>
<li class="chapter" data-level="5.2" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#melanin-binding-regression-3"><i class="fa fa-check"></i><b>5.2</b> Melanin binding (regression)</a>
<ul>
<li class="chapter" data-level="5.2.1" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#model-training-3"><i class="fa fa-check"></i><b>5.2.1</b> Model training</a></li>
<li class="chapter" data-level="5.2.2" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#inner-cross-validation-3"><i class="fa fa-check"></i><b>5.2.2</b> Inner cross-validation</a></li>
<li class="chapter" data-level="5.2.3" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#model-evaluation-3"><i class="fa fa-check"></i><b>5.2.3</b> Model evaluation</a></li>
<li class="chapter" data-level="5.2.4" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#inner-loop-model-selection-3"><i class="fa fa-check"></i><b>5.2.4</b> Inner loop model selection</a>
<ul>
<li class="chapter" data-level="5.2.4.1" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-1-3"><i class="fa fa-check"></i><b>5.2.4.1</b> CV 1</a></li>
<li class="chapter" data-level="5.2.4.2" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-2-3"><i class="fa fa-check"></i><b>5.2.4.2</b> CV 2</a></li>
<li class="chapter" data-level="5.2.4.3" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-3-3"><i class="fa fa-check"></i><b>5.2.4.3</b> CV 3</a></li>
<li class="chapter" data-level="5.2.4.4" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-4-3"><i class="fa fa-check"></i><b>5.2.4.4</b> CV 4</a></li>
<li class="chapter" data-level="5.2.4.5" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-5-3"><i class="fa fa-check"></i><b>5.2.4.5</b> CV 5</a></li>
<li class="chapter" data-level="5.2.4.6" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-6-3"><i class="fa fa-check"></i><b>5.2.4.6</b> CV 6</a></li>
<li class="chapter" data-level="5.2.4.7" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-7-3"><i class="fa fa-check"></i><b>5.2.4.7</b> CV 7</a></li>
<li class="chapter" data-level="5.2.4.8" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-8-3"><i class="fa fa-check"></i><b>5.2.4.8</b> CV 8</a></li>
<li class="chapter" data-level="5.2.4.9" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-9-3"><i class="fa fa-check"></i><b>5.2.4.9</b> CV 9</a></li>
<li class="chapter" data-level="5.2.4.10" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-10-3"><i class="fa fa-check"></i><b>5.2.4.10</b> CV 10</a></li>
</ul></li>
<li class="chapter" data-level="5.2.5" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#final-evaluation-3"><i class="fa fa-check"></i><b>5.2.5</b> Final evaluation</a></li>
</ul></li>
<li class="chapter" data-level="5.3" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cell-penetration-classification-3"><i class="fa fa-check"></i><b>5.3</b> Cell-penetration (classification)</a>
<ul>
<li class="chapter" data-level="5.3.1" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#model-training-4"><i class="fa fa-check"></i><b>5.3.1</b> Model training</a></li>
<li class="chapter" data-level="5.3.2" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#inner-cross-validation-4"><i class="fa fa-check"></i><b>5.3.2</b> Inner cross-validation</a></li>
<li class="chapter" data-level="5.3.3" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#model-evaluation-4"><i class="fa fa-check"></i><b>5.3.3</b> Model evaluation</a></li>
<li class="chapter" data-level="5.3.4" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#inner-loop-model-selection-4"><i class="fa fa-check"></i><b>5.3.4</b> Inner loop model selection</a>
<ul>
<li class="chapter" data-level="5.3.4.1" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-1-4"><i class="fa fa-check"></i><b>5.3.4.1</b> CV 1</a></li>
<li class="chapter" data-level="5.3.4.2" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-2-4"><i class="fa fa-check"></i><b>5.3.4.2</b> CV 2</a></li>
<li class="chapter" data-level="5.3.4.3" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-3-4"><i class="fa fa-check"></i><b>5.3.4.3</b> CV 3</a></li>
<li class="chapter" data-level="5.3.4.4" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-4-4"><i class="fa fa-check"></i><b>5.3.4.4</b> CV 4</a></li>
<li class="chapter" data-level="5.3.4.5" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-5-4"><i class="fa fa-check"></i><b>5.3.4.5</b> CV 5</a></li>
<li class="chapter" data-level="5.3.4.6" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-6-4"><i class="fa fa-check"></i><b>5.3.4.6</b> CV 6</a></li>
<li class="chapter" data-level="5.3.4.7" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-7-4"><i class="fa fa-check"></i><b>5.3.4.7</b> CV 7</a></li>
<li class="chapter" data-level="5.3.4.8" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-8-4"><i class="fa fa-check"></i><b>5.3.4.8</b> CV 8</a></li>
<li class="chapter" data-level="5.3.4.9" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-9-4"><i class="fa fa-check"></i><b>5.3.4.9</b> CV 9</a></li>
<li class="chapter" data-level="5.3.4.10" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-10-4"><i class="fa fa-check"></i><b>5.3.4.10</b> CV 10</a></li>
</ul></li>
<li class="chapter" data-level="5.3.5" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#final-evaluation-4"><i class="fa fa-check"></i><b>5.3.5</b> Final evaluation</a></li>
</ul></li>
<li class="chapter" data-level="5.4" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#toxicity-classification-3"><i class="fa fa-check"></i><b>5.4</b> Toxicity (classification)</a>
<ul>
<li class="chapter" data-level="5.4.1" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#model-training-5"><i class="fa fa-check"></i><b>5.4.1</b> Model training</a></li>
<li class="chapter" data-level="5.4.2" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#inner-cross-validation-5"><i class="fa fa-check"></i><b>5.4.2</b> Inner cross-validation</a></li>
<li class="chapter" data-level="5.4.3" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#model-evaluation-5"><i class="fa fa-check"></i><b>5.4.3</b> Model evaluation</a></li>
<li class="chapter" data-level="5.4.4" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#inner-loop-model-selection-5"><i class="fa fa-check"></i><b>5.4.4</b> Inner loop model selection</a>
<ul>
<li class="chapter" data-level="5.4.4.1" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-1-5"><i class="fa fa-check"></i><b>5.4.4.1</b> CV 1</a></li>
<li class="chapter" data-level="5.4.4.2" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-2-5"><i class="fa fa-check"></i><b>5.4.4.2</b> CV 2</a></li>
<li class="chapter" data-level="5.4.4.3" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-3-5"><i class="fa fa-check"></i><b>5.4.4.3</b> CV 3</a></li>
<li class="chapter" data-level="5.4.4.4" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-4-5"><i class="fa fa-check"></i><b>5.4.4.4</b> CV 4</a></li>
<li class="chapter" data-level="5.4.4.5" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-5-5"><i class="fa fa-check"></i><b>5.4.4.5</b> CV 5</a></li>
<li class="chapter" data-level="5.4.4.6" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-6-5"><i class="fa fa-check"></i><b>5.4.4.6</b> CV 6</a></li>
<li class="chapter" data-level="5.4.4.7" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-7-5"><i class="fa fa-check"></i><b>5.4.4.7</b> CV 7</a></li>
<li class="chapter" data-level="5.4.4.8" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-8-5"><i class="fa fa-check"></i><b>5.4.4.8</b> CV 8</a></li>
<li class="chapter" data-level="5.4.4.9" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-9-5"><i class="fa fa-check"></i><b>5.4.4.9</b> CV 9</a></li>
<li class="chapter" data-level="5.4.4.10" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-10-5"><i class="fa fa-check"></i><b>5.4.4.10</b> CV 10</a></li>
</ul></li>
<li class="chapter" data-level="5.4.5" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#final-evaluation-5"><i class="fa fa-check"></i><b>5.4.5</b> Final evaluation</a></li>
</ul></li>
<li class="chapter" data-level="5.5" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#overall-model-interpretation-1"><i class="fa fa-check"></i><b>5.5</b> Overall model interpretation</a>
<ul>
<li class="chapter" data-level="5.5.1" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#melanin-binding-regression-4"><i class="fa fa-check"></i><b>5.5.1</b> Melanin binding (regression)</a></li>
<li class="chapter" data-level="5.5.2" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cell-penetration-classification-4"><i class="fa fa-check"></i><b>5.5.2</b> Cell-penetration (classification)</a></li>
<li class="chapter" data-level="5.5.3" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#toxicity-classification-4"><i class="fa fa-check"></i><b>5.5.3</b> Toxicity (classification)</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="6" data-path="id_06_small_data_set_demo.html"><a href="id_06_small_data_set_demo.html"><i class="fa fa-check"></i><b>6</b> Small data set demo</a>
<ul>
<li class="chapter" data-level="6.1" data-path="id_06_small_data_set_demo.html"><a href="id_06_small_data_set_demo.html#setup"><i class="fa fa-check"></i><b>6.1</b> Setup</a>
<ul>
<li class="chapter" data-level="6.1.1" data-path="id_06_small_data_set_demo.html"><a href="id_06_small_data_set_demo.html#load-libraries"><i class="fa fa-check"></i><b>6.1.1</b> Load libraries</a></li>
<li class="chapter" data-level="6.1.2" data-path="id_06_small_data_set_demo.html"><a href="id_06_small_data_set_demo.html#aic-functions-1"><i class="fa fa-check"></i><b>6.1.2</b> AIC functions</a></li>
<li class="chapter" data-level="6.1.3" data-path="id_06_small_data_set_demo.html"><a href="id_06_small_data_set_demo.html#model-parameters"><i class="fa fa-check"></i><b>6.1.3</b> Model parameters</a></li>
</ul></li>
<li class="chapter" data-level="6.2" data-path="id_06_small_data_set_demo.html"><a href="id_06_small_data_set_demo.html#variable-reduction-3"><i class="fa fa-check"></i><b>6.2</b> Variable reduction</a></li>
<li class="chapter" data-level="6.3" data-path="id_06_small_data_set_demo.html"><a href="id_06_small_data_set_demo.html#model-training-6"><i class="fa fa-check"></i><b>6.3</b> Model training</a></li>
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<h1>
<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">Multifunctional peptide engineering</a>
</h1>
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<section class="normal" id="section-">
<div id="id_01_pilot_peptide_array" class="section level1 hasAnchor" number="1">
<h1><span class="header-section-number">Section 1</span> Melanin binding pilot peptide array<a href="id_01_pilot_peptide_array.html#id_01_pilot_peptide_array" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<div class="sourceCode" id="cb2"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb2-1"><a href="id_01_pilot_peptide_array.html#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(seqinr)</span>
<span id="cb2-2"><a href="id_01_pilot_peptide_array.html#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(Peptides)</span>
<span id="cb2-3"><a href="id_01_pilot_peptide_array.html#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(stringr)</span>
<span id="cb2-4"><a href="id_01_pilot_peptide_array.html#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(protr)</span>
<span id="cb2-5"><a href="id_01_pilot_peptide_array.html#cb2-5" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(plyr)</span>
<span id="cb2-6"><a href="id_01_pilot_peptide_array.html#cb2-6" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(randomForest)</span>
<span id="cb2-7"><a href="id_01_pilot_peptide_array.html#cb2-7" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggplot2)</span></code></pre></div>
<div id="overview" class="section level2 hasAnchor" number="1.1">
<h2><span class="header-section-number">1.1</span> Overview<a href="id_01_pilot_peptide_array.html#overview" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p><img src="figures/mb_pilot_overview.png" width="100%" style="display: block; margin: auto;" /></p>
</div>
<div id="generating-ml-input" class="section level2 hasAnchor" number="1.2">
<h2><span class="header-section-number">1.2</span> Generating ML input<a href="id_01_pilot_peptide_array.html#generating-ml-input" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div class="sourceCode" id="cb3"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb3-1"><a href="id_01_pilot_peptide_array.html#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="co"># --------------</span></span>
<span id="cb3-2"><a href="id_01_pilot_peptide_array.html#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="co"># Peptides_2.4.4</span></span>
<span id="cb3-3"><a href="id_01_pilot_peptide_array.html#cb3-3" aria-hidden="true" tabindex="-1"></a><span class="co"># --------------</span></span>
<span id="cb3-4"><a href="id_01_pilot_peptide_array.html#cb3-4" aria-hidden="true" tabindex="-1"></a><span class="co"># read in fasta file</span></span>
<span id="cb3-5"><a href="id_01_pilot_peptide_array.html#cb3-5" aria-hidden="true" tabindex="-1"></a>peptides <span class="ot"><-</span> <span class="fu">read.fasta</span>(<span class="st">"./other_data/mb_pilot_peptide_array.fasta"</span>, <span class="at">seqtype =</span> <span class="st">"AA"</span>, <span class="at">as.string =</span> <span class="cn">TRUE</span>, <span class="at">set.attributes =</span> <span class="cn">FALSE</span>)</span>
<span id="cb3-6"><a href="id_01_pilot_peptide_array.html#cb3-6" aria-hidden="true" tabindex="-1"></a><span class="co"># Molecular weight</span></span>
<span id="cb3-7"><a href="id_01_pilot_peptide_array.html#cb3-7" aria-hidden="true" tabindex="-1"></a>weights <span class="ot"><-</span> <span class="fu">as.matrix</span>(<span class="fu">sapply</span>(peptides, <span class="cf">function</span>(x) <span class="fu">mw</span>(x, <span class="at">monoisotopic =</span> <span class="cn">FALSE</span>)))</span>
<span id="cb3-8"><a href="id_01_pilot_peptide_array.html#cb3-8" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(weights) <span class="ot"><-</span> <span class="st">"weight"</span></span>
<span id="cb3-9"><a href="id_01_pilot_peptide_array.html#cb3-9" aria-hidden="true" tabindex="-1"></a><span class="co"># Amino acid composition</span></span>
<span id="cb3-10"><a href="id_01_pilot_peptide_array.html#cb3-10" aria-hidden="true" tabindex="-1"></a>aa.comp <span class="ot"><-</span> <span class="fu">sapply</span>(peptides, <span class="cf">function</span>(x) <span class="fu">aaComp</span>(x))</span>
<span id="cb3-11"><a href="id_01_pilot_peptide_array.html#cb3-11" aria-hidden="true" tabindex="-1"></a>aa.comp.matrix <span class="ot"><-</span> <span class="fu">t</span>(<span class="fu">sapply</span>(aa.comp, <span class="cf">function</span>(x) x[, <span class="st">"Mole%"</span>]))</span>
<span id="cb3-12"><a href="id_01_pilot_peptide_array.html#cb3-12" aria-hidden="true" tabindex="-1"></a><span class="co"># Isoelectric point</span></span>
<span id="cb3-13"><a href="id_01_pilot_peptide_array.html#cb3-13" aria-hidden="true" tabindex="-1"></a>pI.values <span class="ot"><-</span> <span class="fu">as.matrix</span>(<span class="fu">sapply</span>(peptides, <span class="cf">function</span>(x) <span class="fu">pI</span>(x, <span class="at">pKscale =</span> <span class="st">"EMBOSS"</span>)))</span>
<span id="cb3-14"><a href="id_01_pilot_peptide_array.html#cb3-14" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(pI.values) <span class="ot"><-</span> <span class="st">"pI.value"</span></span>
<span id="cb3-15"><a href="id_01_pilot_peptide_array.html#cb3-15" aria-hidden="true" tabindex="-1"></a><span class="co"># Hydrophobicity</span></span>
<span id="cb3-16"><a href="id_01_pilot_peptide_array.html#cb3-16" aria-hidden="true" tabindex="-1"></a>hydrophobicity.values <span class="ot"><-</span> <span class="fu">as.matrix</span>(<span class="fu">sapply</span>(peptides, <span class="cf">function</span>(x) <span class="fu">hydrophobicity</span>(x, <span class="at">scale =</span> <span class="st">"KyteDoolittle"</span>)))</span>
<span id="cb3-17"><a href="id_01_pilot_peptide_array.html#cb3-17" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(hydrophobicity.values) <span class="ot"><-</span> <span class="st">"hydrophobicity.value"</span></span>
<span id="cb3-18"><a href="id_01_pilot_peptide_array.html#cb3-18" aria-hidden="true" tabindex="-1"></a><span class="co"># Net charge at pH 7</span></span>
<span id="cb3-19"><a href="id_01_pilot_peptide_array.html#cb3-19" aria-hidden="true" tabindex="-1"></a>net.charges <span class="ot"><-</span> <span class="fu">as.matrix</span>(<span class="fu">sapply</span>(peptides, <span class="cf">function</span>(x) <span class="fu">charge</span>(x, <span class="at">pH =</span> <span class="dv">7</span>, <span class="at">pKscale =</span> <span class="st">"EMBOSS"</span>)))</span>
<span id="cb3-20"><a href="id_01_pilot_peptide_array.html#cb3-20" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(net.charges) <span class="ot"><-</span> <span class="st">"net.charge"</span></span>
<span id="cb3-21"><a href="id_01_pilot_peptide_array.html#cb3-21" aria-hidden="true" tabindex="-1"></a><span class="co"># Boman index</span></span>
<span id="cb3-22"><a href="id_01_pilot_peptide_array.html#cb3-22" aria-hidden="true" tabindex="-1"></a>boman.indices <span class="ot"><-</span> <span class="fu">as.matrix</span>(<span class="fu">sapply</span>(peptides, <span class="cf">function</span>(x) <span class="fu">boman</span>(x)))</span>
<span id="cb3-23"><a href="id_01_pilot_peptide_array.html#cb3-23" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(boman.indices) <span class="ot"><-</span> <span class="st">"boman.index"</span></span>
<span id="cb3-24"><a href="id_01_pilot_peptide_array.html#cb3-24" aria-hidden="true" tabindex="-1"></a><span class="co"># combine peptides results</span></span>
<span id="cb3-25"><a href="id_01_pilot_peptide_array.html#cb3-25" aria-hidden="true" tabindex="-1"></a>peptides_res <span class="ot"><-</span> <span class="fu">data.frame</span>(<span class="fu">cbind</span>(weights, aa.comp.matrix, pI.values, hydrophobicity.values, net.charges, boman.indices))</span>
<span id="cb3-26"><a href="id_01_pilot_peptide_array.html#cb3-26" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-27"><a href="id_01_pilot_peptide_array.html#cb3-27" aria-hidden="true" tabindex="-1"></a><span class="co"># -----------</span></span>
<span id="cb3-28"><a href="id_01_pilot_peptide_array.html#cb3-28" aria-hidden="true" tabindex="-1"></a><span class="co"># protr_1.6-2</span></span>
<span id="cb3-29"><a href="id_01_pilot_peptide_array.html#cb3-29" aria-hidden="true" tabindex="-1"></a><span class="co"># -----------</span></span>
<span id="cb3-30"><a href="id_01_pilot_peptide_array.html#cb3-30" aria-hidden="true" tabindex="-1"></a>length <span class="ot"><-</span> <span class="dv">7</span></span>
<span id="cb3-31"><a href="id_01_pilot_peptide_array.html#cb3-31" aria-hidden="true" tabindex="-1"></a><span class="co"># read in FASTA file</span></span>
<span id="cb3-32"><a href="id_01_pilot_peptide_array.html#cb3-32" aria-hidden="true" tabindex="-1"></a>sequences <span class="ot"><-</span> <span class="fu">readFASTA</span>(<span class="st">"./other_data/mb_pilot_peptide_array.fasta"</span>)</span>
<span id="cb3-33"><a href="id_01_pilot_peptide_array.html#cb3-33" aria-hidden="true" tabindex="-1"></a>sequences <span class="ot"><-</span> sequences[<span class="fu">unlist</span>(<span class="fu">lapply</span>(sequences, <span class="cf">function</span>(x) <span class="fu">nchar</span>(x) <span class="sc">></span> <span class="dv">1</span>))]</span>
<span id="cb3-34"><a href="id_01_pilot_peptide_array.html#cb3-34" aria-hidden="true" tabindex="-1"></a><span class="co"># calculate amino acid composition descriptors (dim = 20)</span></span>
<span id="cb3-35"><a href="id_01_pilot_peptide_array.html#cb3-35" aria-hidden="true" tabindex="-1"></a>x1 <span class="ot"><-</span> <span class="fu">t</span>(<span class="fu">sapply</span>(sequences, extractAAC))</span>
<span id="cb3-36"><a href="id_01_pilot_peptide_array.html#cb3-36" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(x1)[<span class="fu">colnames</span>(x1) <span class="sc">==</span> <span class="st">"Y"</span>] <span class="ot"><-</span> <span class="st">"Y_tyrosine"</span></span>
<span id="cb3-37"><a href="id_01_pilot_peptide_array.html#cb3-37" aria-hidden="true" tabindex="-1"></a><span class="co"># calculate dipeptide composition descriptors (dim = 400)</span></span>
<span id="cb3-38"><a href="id_01_pilot_peptide_array.html#cb3-38" aria-hidden="true" tabindex="-1"></a>x2 <span class="ot"><-</span> <span class="fu">t</span>(<span class="fu">sapply</span>(sequences, extractDC))</span>
<span id="cb3-39"><a href="id_01_pilot_peptide_array.html#cb3-39" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(x2)[<span class="fu">colnames</span>(x2) <span class="sc">==</span> <span class="st">"NA"</span>] <span class="ot"><-</span> <span class="st">"NA_dipeptide"</span></span>
<span id="cb3-40"><a href="id_01_pilot_peptide_array.html#cb3-40" aria-hidden="true" tabindex="-1"></a><span class="co"># calculate Moreau-Broto autocorrelation descriptors (dim = 8 * (length - 1))</span></span>
<span id="cb3-41"><a href="id_01_pilot_peptide_array.html#cb3-41" aria-hidden="true" tabindex="-1"></a>x3 <span class="ot"><-</span> <span class="fu">t</span>(<span class="fu">sapply</span>(sequences, extractMoreauBroto, <span class="at">nlag =</span> length <span class="sc">-</span> 1L))</span>
<span id="cb3-42"><a href="id_01_pilot_peptide_array.html#cb3-42" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(x3) <span class="ot"><-</span> <span class="fu">paste</span>(<span class="st">"moreau_broto"</span>, <span class="fu">colnames</span>(x3), <span class="at">sep =</span> <span class="st">"_"</span>)</span>
<span id="cb3-43"><a href="id_01_pilot_peptide_array.html#cb3-43" aria-hidden="true" tabindex="-1"></a><span class="co"># calculate composition descriptors (dim = 21)</span></span>
<span id="cb3-44"><a href="id_01_pilot_peptide_array.html#cb3-44" aria-hidden="true" tabindex="-1"></a>x4 <span class="ot"><-</span> <span class="fu">t</span>(<span class="fu">sapply</span>(sequences, extractCTDC))</span>
<span id="cb3-45"><a href="id_01_pilot_peptide_array.html#cb3-45" aria-hidden="true" tabindex="-1"></a><span class="co"># calculate transition descriptors (dim = 21)</span></span>
<span id="cb3-46"><a href="id_01_pilot_peptide_array.html#cb3-46" aria-hidden="true" tabindex="-1"></a>x5 <span class="ot"><-</span> <span class="fu">t</span>(<span class="fu">sapply</span>(sequences, extractCTDT))</span>
<span id="cb3-47"><a href="id_01_pilot_peptide_array.html#cb3-47" aria-hidden="true" tabindex="-1"></a><span class="co"># calculate distribution descriptors (dim = 105)</span></span>
<span id="cb3-48"><a href="id_01_pilot_peptide_array.html#cb3-48" aria-hidden="true" tabindex="-1"></a>x6 <span class="ot"><-</span> <span class="fu">t</span>(<span class="fu">sapply</span>(sequences, extractCTDD))</span>
<span id="cb3-49"><a href="id_01_pilot_peptide_array.html#cb3-49" aria-hidden="true" tabindex="-1"></a><span class="co"># calculate conjoint triad descriptors (dim = 343)</span></span>
<span id="cb3-50"><a href="id_01_pilot_peptide_array.html#cb3-50" aria-hidden="true" tabindex="-1"></a>x7 <span class="ot"><-</span> <span class="fu">t</span>(<span class="fu">sapply</span>(sequences, extractCTriad))</span>
<span id="cb3-51"><a href="id_01_pilot_peptide_array.html#cb3-51" aria-hidden="true" tabindex="-1"></a><span class="co"># calculate sequence-order-coupling numbers (dim = 2 * (length - 1))</span></span>
<span id="cb3-52"><a href="id_01_pilot_peptide_array.html#cb3-52" aria-hidden="true" tabindex="-1"></a>x8 <span class="ot"><-</span> <span class="fu">t</span>(<span class="fu">sapply</span>(sequences, extractSOCN, <span class="at">nlag =</span> length <span class="sc">-</span> 1L))</span>
<span id="cb3-53"><a href="id_01_pilot_peptide_array.html#cb3-53" aria-hidden="true" tabindex="-1"></a><span class="co"># calculate quasi-sequence-order descriptors (dim = 40 + 2 * (length - 1))</span></span>
<span id="cb3-54"><a href="id_01_pilot_peptide_array.html#cb3-54" aria-hidden="true" tabindex="-1"></a>x9 <span class="ot"><-</span> <span class="fu">t</span>(<span class="fu">sapply</span>(sequences, extractQSO, <span class="at">nlag =</span> length <span class="sc">-</span> 1L))</span>
<span id="cb3-55"><a href="id_01_pilot_peptide_array.html#cb3-55" aria-hidden="true" tabindex="-1"></a><span class="co"># calculate pseudo-amino acid composition (dim = 20 + (length - 1))</span></span>
<span id="cb3-56"><a href="id_01_pilot_peptide_array.html#cb3-56" aria-hidden="true" tabindex="-1"></a>x10 <span class="ot"><-</span> <span class="fu">t</span>(<span class="fu">sapply</span>(sequences, extractPAAC, <span class="at">lambda =</span> length <span class="sc">-</span> 1L))</span>
<span id="cb3-57"><a href="id_01_pilot_peptide_array.html#cb3-57" aria-hidden="true" tabindex="-1"></a><span class="co"># calculate amphiphilic pseudo-amino acid composition (dim = 20 + 2 * (length - 1))</span></span>
<span id="cb3-58"><a href="id_01_pilot_peptide_array.html#cb3-58" aria-hidden="true" tabindex="-1"></a>x11 <span class="ot"><-</span> <span class="fu">t</span>(<span class="fu">sapply</span>(sequences, extractAPAAC, <span class="at">lambda =</span> length <span class="sc">-</span> 1L))</span>
<span id="cb3-59"><a href="id_01_pilot_peptide_array.html#cb3-59" aria-hidden="true" tabindex="-1"></a><span class="co"># combine all of the result datasets</span></span>
<span id="cb3-60"><a href="id_01_pilot_peptide_array.html#cb3-60" aria-hidden="true" tabindex="-1"></a>protr_res <span class="ot"><-</span> <span class="fu">data.frame</span>(<span class="fu">cbind</span>(x1, x2, x3, x4, x5, x6, x7, x8, x9, x10, x11))</span>
<span id="cb3-61"><a href="id_01_pilot_peptide_array.html#cb3-61" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-62"><a href="id_01_pilot_peptide_array.html#cb3-62" aria-hidden="true" tabindex="-1"></a>labels <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./other_data/mb_pilot_peptide_array_labels.csv"</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb3-63"><a href="id_01_pilot_peptide_array.html#cb3-63" aria-hidden="true" tabindex="-1"></a>merge.all <span class="ot"><-</span> <span class="cf">function</span>(x, ..., <span class="at">by =</span> <span class="st">"row.names"</span>) {</span>
<span id="cb3-64"><a href="id_01_pilot_peptide_array.html#cb3-64" aria-hidden="true" tabindex="-1"></a> L <span class="ot"><-</span> <span class="fu">list</span>(...)</span>
<span id="cb3-65"><a href="id_01_pilot_peptide_array.html#cb3-65" aria-hidden="true" tabindex="-1"></a> <span class="cf">for</span> (i <span class="cf">in</span> <span class="fu">seq_along</span>(L)) {</span>
<span id="cb3-66"><a href="id_01_pilot_peptide_array.html#cb3-66" aria-hidden="true" tabindex="-1"></a> x <span class="ot"><-</span> <span class="fu">merge</span>(x, L[[i]], <span class="at">by =</span> by)</span>
<span id="cb3-67"><a href="id_01_pilot_peptide_array.html#cb3-67" aria-hidden="true" tabindex="-1"></a> <span class="fu">rownames</span>(x) <span class="ot"><-</span> x<span class="sc">$</span>Row.names</span>
<span id="cb3-68"><a href="id_01_pilot_peptide_array.html#cb3-68" aria-hidden="true" tabindex="-1"></a> x<span class="sc">$</span>Row.names <span class="ot"><-</span> <span class="cn">NULL</span></span>
<span id="cb3-69"><a href="id_01_pilot_peptide_array.html#cb3-69" aria-hidden="true" tabindex="-1"></a> }</span>
<span id="cb3-70"><a href="id_01_pilot_peptide_array.html#cb3-70" aria-hidden="true" tabindex="-1"></a> <span class="fu">return</span>(x)</span>
<span id="cb3-71"><a href="id_01_pilot_peptide_array.html#cb3-71" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb3-72"><a href="id_01_pilot_peptide_array.html#cb3-72" aria-hidden="true" tabindex="-1"></a>data <span class="ot"><-</span> <span class="fu">merge.all</span>(peptides_res, protr_res, labels)</span>
<span id="cb3-73"><a href="id_01_pilot_peptide_array.html#cb3-73" aria-hidden="true" tabindex="-1"></a><span class="fu">write.csv</span>(data, <span class="at">file =</span> <span class="st">"./data/mb_pilot_peptide_array_ml_input.csv"</span>)</span></code></pre></div>
</div>
<div id="training-initial-rf-model" class="section level2 hasAnchor" number="1.3">
<h2><span class="header-section-number">1.3</span> Training initial RF model<a href="id_01_pilot_peptide_array.html#training-initial-rf-model" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div class="sourceCode" id="cb4"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb4-1"><a href="id_01_pilot_peptide_array.html#cb4-1" aria-hidden="true" tabindex="-1"></a>data <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./data/mb_pilot_peptide_array_ml_input.csv"</span>, <span class="at">check.names =</span> <span class="cn">FALSE</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb4-2"><a href="id_01_pilot_peptide_array.html#cb4-2" aria-hidden="true" tabindex="-1"></a>predictor_variables <span class="ot"><-</span> <span class="fu">subset</span>(data, <span class="at">select =</span> <span class="sc">-</span>category)</span>
<span id="cb4-3"><a href="id_01_pilot_peptide_array.html#cb4-3" aria-hidden="true" tabindex="-1"></a>response_variable <span class="ot"><-</span> <span class="fu">factor</span>(data<span class="sc">$</span>category, <span class="at">levels =</span> <span class="fu">c</span>(<span class="st">"non-bind"</span>, <span class="st">"bind"</span>))</span>
<span id="cb4-4"><a href="id_01_pilot_peptide_array.html#cb4-4" aria-hidden="true" tabindex="-1"></a><span class="co"># impute missing values</span></span>
<span id="cb4-5"><a href="id_01_pilot_peptide_array.html#cb4-5" aria-hidden="true" tabindex="-1"></a>response_variable <span class="ot"><-</span> <span class="fu">na.roughfix</span>(response_variable)</span>
<span id="cb4-6"><a href="id_01_pilot_peptide_array.html#cb4-6" aria-hidden="true" tabindex="-1"></a><span class="co"># perform balance sampling</span></span>
<span id="cb4-7"><a href="id_01_pilot_peptide_array.html#cb4-7" aria-hidden="true" tabindex="-1"></a>samp_size <span class="ot"><-</span> <span class="fu">min</span>(<span class="fu">table</span>(response_variable))</span></code></pre></div>
<div class="sourceCode" id="cb5"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb5-1"><a href="id_01_pilot_peptide_array.html#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="co"># build RF model</span></span>
<span id="cb5-2"><a href="id_01_pilot_peptide_array.html#cb5-2" aria-hidden="true" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">22</span>)</span>
<span id="cb5-3"><a href="id_01_pilot_peptide_array.html#cb5-3" aria-hidden="true" tabindex="-1"></a>ntree <span class="ot"><-</span> <span class="dv">100000</span></span>
<span id="cb5-4"><a href="id_01_pilot_peptide_array.html#cb5-4" aria-hidden="true" tabindex="-1"></a>rf <span class="ot"><-</span> <span class="fu">randomForest</span>(</span>
<span id="cb5-5"><a href="id_01_pilot_peptide_array.html#cb5-5" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> predictor_variables, <span class="at">y =</span> response_variable, <span class="at">ntree =</span> ntree, <span class="at">sampsize =</span> <span class="fu">rep</span>(samp_size, <span class="dv">2</span>),</span>
<span id="cb5-6"><a href="id_01_pilot_peptide_array.html#cb5-6" aria-hidden="true" tabindex="-1"></a> <span class="at">importance =</span> <span class="cn">TRUE</span>, <span class="at">proximity =</span> <span class="cn">TRUE</span>, <span class="at">do.trace =</span> <span class="fl">0.1</span> <span class="sc">*</span> ntree</span>
<span id="cb5-7"><a href="id_01_pilot_peptide_array.html#cb5-7" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb5-8"><a href="id_01_pilot_peptide_array.html#cb5-8" aria-hidden="true" tabindex="-1"></a><span class="fu">save</span>(rf, <span class="at">file =</span> <span class="st">"./rdata/mb_pilot_rf.RData"</span>)</span></code></pre></div>
</div>
<div id="melanin-binding-variable-importance" class="section level2 hasAnchor" number="1.4">
<h2><span class="header-section-number">1.4</span> Melanin binding variable importance<a href="id_01_pilot_peptide_array.html#melanin-binding-variable-importance" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div class="sourceCode" id="cb6"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb6-1"><a href="id_01_pilot_peptide_array.html#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="fu">load</span>(<span class="at">file =</span> <span class="st">"./rdata/mb_pilot_rf.RData"</span>)</span>
<span id="cb6-2"><a href="id_01_pilot_peptide_array.html#cb6-2" aria-hidden="true" tabindex="-1"></a>imp_ds <span class="ot"><-</span> <span class="fu">as.data.frame</span>(<span class="fu">importance</span>(rf)[, <span class="st">"MeanDecreaseAccuracy"</span>, <span class="at">drop =</span> <span class="cn">FALSE</span>])</span>
<span id="cb6-3"><a href="id_01_pilot_peptide_array.html#cb6-3" aria-hidden="true" tabindex="-1"></a>imp_ds<span class="sc">$</span><span class="st">`</span><span class="at">Feature</span><span class="st">`</span> <span class="ot"><-</span> <span class="fu">rownames</span>(imp_ds)</span>
<span id="cb6-4"><a href="id_01_pilot_peptide_array.html#cb6-4" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(imp_ds) <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"Mean decrease accuracy"</span>, <span class="st">"Feature"</span>)</span>
<span id="cb6-5"><a href="id_01_pilot_peptide_array.html#cb6-5" aria-hidden="true" tabindex="-1"></a>imp_ds <span class="ot"><-</span> imp_ds[<span class="fu">order</span>(<span class="sc">-</span>imp_ds<span class="sc">$</span><span class="st">`</span><span class="at">Mean decrease accuracy</span><span class="st">`</span>), ][<span class="dv">1</span><span class="sc">:</span><span class="dv">20</span>, ]</span>
<span id="cb6-6"><a href="id_01_pilot_peptide_array.html#cb6-6" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-7"><a href="id_01_pilot_peptide_array.html#cb6-7" aria-hidden="true" tabindex="-1"></a>p <span class="ot"><-</span> <span class="fu">ggplot</span>(imp_ds, <span class="fu">aes</span>(<span class="at">x =</span> <span class="fu">reorder</span>(<span class="st">`</span><span class="at">Feature</span><span class="st">`</span>, <span class="st">`</span><span class="at">Mean decrease accuracy</span><span class="st">`</span>), <span class="at">y =</span> <span class="st">`</span><span class="at">Mean decrease accuracy</span><span class="st">`</span>)) <span class="sc">+</span></span>
<span id="cb6-8"><a href="id_01_pilot_peptide_array.html#cb6-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_col</span>(<span class="at">color =</span> <span class="st">"grey10"</span>, <span class="at">fill =</span> <span class="st">"#f5b8b8"</span>, <span class="at">size =</span> <span class="fl">0.2</span>) <span class="sc">+</span></span>
<span id="cb6-9"><a href="id_01_pilot_peptide_array.html#cb6-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_text</span>(<span class="fu">aes</span>(<span class="at">label =</span> <span class="fu">sprintf</span>(<span class="st">"%.2f"</span>, <span class="st">`</span><span class="at">Mean decrease accuracy</span><span class="st">`</span>)), <span class="at">nudge_y =</span> <span class="fl">4.2</span>, <span class="at">size =</span> <span class="dv">3</span>) <span class="sc">+</span></span>
<span id="cb6-10"><a href="id_01_pilot_peptide_array.html#cb6-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">coord_flip</span>() <span class="sc">+</span></span>
<span id="cb6-11"><a href="id_01_pilot_peptide_array.html#cb6-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">ylim</span>(<span class="dv">0</span>, <span class="fu">max</span>(imp_ds<span class="sc">$</span><span class="st">`</span><span class="at">Mean decrease accuracy</span><span class="st">`</span>) <span class="sc">+</span> <span class="dv">5</span>) <span class="sc">+</span></span>
<span id="cb6-12"><a href="id_01_pilot_peptide_array.html#cb6-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
<span id="cb6-13"><a href="id_01_pilot_peptide_array.html#cb6-13" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb6-14"><a href="id_01_pilot_peptide_array.html#cb6-14" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.major =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb6-15"><a href="id_01_pilot_peptide_array.html#cb6-15" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.minor =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb6-16"><a href="id_01_pilot_peptide_array.html#cb6-16" aria-hidden="true" tabindex="-1"></a> <span class="at">strip.background =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb6-17"><a href="id_01_pilot_peptide_array.html#cb6-17" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.border =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb6-18"><a href="id_01_pilot_peptide_array.html#cb6-18" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.line =</span> <span class="fu">element_line</span>(<span class="at">color =</span> <span class="st">"black"</span>),</span>
<span id="cb6-19"><a href="id_01_pilot_peptide_array.html#cb6-19" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.text =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">10</span>),</span>
<span id="cb6-20"><a href="id_01_pilot_peptide_array.html#cb6-20" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.title =</span> <span class="fu">element_text</span>(<span class="at">hjust =</span> <span class="fl">0.5</span>, <span class="at">size =</span> <span class="dv">18</span>),</span>
<span id="cb6-21"><a href="id_01_pilot_peptide_array.html#cb6-21" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.margin =</span> ggplot2<span class="sc">::</span><span class="fu">margin</span>(<span class="dv">10</span>, <span class="dv">10</span>, <span class="dv">10</span>, <span class="dv">0</span>, <span class="st">"pt"</span>),</span>
<span id="cb6-22"><a href="id_01_pilot_peptide_array.html#cb6-22" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.x =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">18</span>),</span>
<span id="cb6-23"><a href="id_01_pilot_peptide_array.html#cb6-23" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.y =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">18</span>),</span>
<span id="cb6-24"><a href="id_01_pilot_peptide_array.html#cb6-24" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text.x =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">12</span>),</span>
<span id="cb6-25"><a href="id_01_pilot_peptide_array.html#cb6-25" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text.y =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">12</span>),</span>
<span id="cb6-26"><a href="id_01_pilot_peptide_array.html#cb6-26" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.title =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">14</span>),</span>
<span id="cb6-27"><a href="id_01_pilot_peptide_array.html#cb6-27" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.position =</span> <span class="fu">c</span>(<span class="fl">0.85</span>, <span class="fl">0.5</span>)</span>
<span id="cb6-28"><a href="id_01_pilot_peptide_array.html#cb6-28" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb6-29"><a href="id_01_pilot_peptide_array.html#cb6-29" aria-hidden="true" tabindex="-1"></a> <span class="fu">xlab</span>(<span class="st">""</span>) <span class="sc">+</span></span>
<span id="cb6-30"><a href="id_01_pilot_peptide_array.html#cb6-30" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggtitle</span>(<span class="st">""</span>)</span></code></pre></div>
<p><img src="figures/Fig%201%20mb%20pilot%20var%20imp.png" width="100%" style="display: block; margin: auto;" /></p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb7-1"><a href="id_01_pilot_peptide_array.html#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="fu">sessionInfo</span>()</span></code></pre></div>
<pre><code>## R version 4.2.2 (2022-10-31)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur ... 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ggplot2_3.3.6 randomForest_4.7-1.1 plyr_1.8.7
## [4] protr_1.6-2 stringr_1.4.1 Peptides_2.4.4
## [7] seqinr_4.2-16
##
## loaded via a namespace (and not attached):
## [1] styler_1.8.0 tidyselect_1.1.2 xfun_0.32 bslib_0.4.0
## [5] purrr_0.3.4 colorspace_2.0-3 vctrs_0.4.1 generics_0.1.3
## [9] htmltools_0.5.3 yaml_2.3.5 utf8_1.2.2 rlang_1.0.4
## [13] R.oo_1.25.0 jquerylib_0.1.4 pillar_1.8.1 glue_1.6.2
## [17] withr_2.5.0 DBI_1.1.3 R.utils_2.12.0 R.cache_0.16.0
## [21] lifecycle_1.0.1 munsell_0.5.0 gtable_0.3.0 R.methodsS3_1.8.2
## [25] codetools_0.2-18 evaluate_0.16 knitr_1.40 fastmap_1.1.0
## [29] fansi_1.0.3 highr_0.9 Rcpp_1.0.9 scales_1.2.1
## [33] cachem_1.0.6 jsonlite_1.8.0 digest_0.6.29 stringi_1.7.8
## [37] bookdown_0.28 dplyr_1.0.9 grid_4.2.2 ade4_1.7-19
## [41] cli_3.3.0 tools_4.2.2 magrittr_2.0.3 sass_0.4.2
## [45] tibble_3.1.8 pkgconfig_2.0.3 MASS_7.3-58.1 assertthat_0.2.1
## [49] rmarkdown_2.16 rstudioapi_0.14 R6_2.5.1 compiler_4.2.2</code></pre>
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