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<title>7.6 Exercises | Computational Genomics with R</title>
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<li><a href="./">Computational Genomics with R</a></li>
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<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Preface</a><ul>
<li class="chapter" data-level="" data-path="who-is-this-book-for.html"><a href="who-is-this-book-for.html"><i class="fa fa-check"></i>Who is this book for?</a><ul>
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<li class="chapter" data-level="" data-path="structure-of-the-book.html"><a href="structure-of-the-book.html"><i class="fa fa-check"></i>Structure of the book</a></li>
<li class="chapter" data-level="" data-path="software-information-and-conventions.html"><a href="software-information-and-conventions.html"><i class="fa fa-check"></i>Software information and conventions</a><ul>
<li class="chapter" data-level="" data-path="software-information-and-conventions.html"><a href="software-information-and-conventions.html#assignment-operator-convention"><i class="fa fa-check"></i>Assignment operator convention</a></li>
<li class="chapter" data-level="" data-path="software-information-and-conventions.html"><a href="software-information-and-conventions.html#packages-needed-to-run-the-book-code"><i class="fa fa-check"></i>Packages needed to run the book code</a></li>
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<li class="chapter" data-level="" data-path="data-for-the-book.html"><a href="data-for-the-book.html"><i class="fa fa-check"></i>Data for the book</a></li>
<li class="chapter" data-level="" data-path="exercises-in-the-book.html"><a href="exercises-in-the-book.html"><i class="fa fa-check"></i>Exercises in the book</a></li>
<li class="chapter" data-level="" data-path="reproducibility-statement.html"><a href="reproducibility-statement.html"><i class="fa fa-check"></i>Reproducibility statement</a></li>
<li class="chapter" data-level="" data-path="acknowledgements.html"><a href="acknowledgements.html"><i class="fa fa-check"></i>Acknowledgements</a></li>
<li class="chapter" data-level="" data-path="how-to-contribute.html"><a href="how-to-contribute.html"><i class="fa fa-check"></i>How to contribute</a></li>
</ul></li>
<li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
<li class="chapter" data-level="1" data-path="intro.html"><a href="intro.html"><i class="fa fa-check"></i><b>1</b> Introduction to Genomics</a><ul>
<li class="chapter" data-level="1.1" data-path="genes-dna-and-central-dogma.html"><a href="genes-dna-and-central-dogma.html"><i class="fa fa-check"></i><b>1.1</b> Genes, DNA and central dogma</a><ul>
<li class="chapter" data-level="1.1.1" data-path="genes-dna-and-central-dogma.html"><a href="genes-dna-and-central-dogma.html#what-is-a-genome"><i class="fa fa-check"></i><b>1.1.1</b> What is a genome?</a></li>
<li class="chapter" data-level="1.1.2" data-path="genes-dna-and-central-dogma.html"><a href="genes-dna-and-central-dogma.html#what-is-a-gene"><i class="fa fa-check"></i><b>1.1.2</b> What is a gene?</a></li>
<li class="chapter" data-level="1.1.3" data-path="genes-dna-and-central-dogma.html"><a href="genes-dna-and-central-dogma.html#how-are-genes-controlled-transcriptional-and-post-transcriptional-regulation"><i class="fa fa-check"></i><b>1.1.3</b> How are genes controlled? Transcriptional and post-transcriptional regulation</a></li>
<li class="chapter" data-level="1.1.4" data-path="genes-dna-and-central-dogma.html"><a href="genes-dna-and-central-dogma.html#what-does-a-gene-look-like"><i class="fa fa-check"></i><b>1.1.4</b> What does a gene look like?</a></li>
</ul></li>
<li class="chapter" data-level="1.2" data-path="elements-of-gene-regulation.html"><a href="elements-of-gene-regulation.html"><i class="fa fa-check"></i><b>1.2</b> Elements of gene regulation</a><ul>
<li class="chapter" data-level="1.2.1" data-path="elements-of-gene-regulation.html"><a href="elements-of-gene-regulation.html#transcriptional-regulation"><i class="fa fa-check"></i><b>1.2.1</b> Transcriptional regulation</a></li>
<li class="chapter" data-level="1.2.2" data-path="elements-of-gene-regulation.html"><a href="elements-of-gene-regulation.html#post-transcriptional-regulation"><i class="fa fa-check"></i><b>1.2.2</b> Post-transcriptional regulation</a></li>
</ul></li>
<li class="chapter" data-level="1.3" data-path="shaping-the-genome-dna-mutation.html"><a href="shaping-the-genome-dna-mutation.html"><i class="fa fa-check"></i><b>1.3</b> Shaping the genome: DNA mutation</a></li>
<li class="chapter" data-level="1.4" data-path="high-throughput-experimental-methods-in-genomics.html"><a href="high-throughput-experimental-methods-in-genomics.html"><i class="fa fa-check"></i><b>1.4</b> High-throughput experimental methods in genomics</a><ul>
<li class="chapter" data-level="1.4.1" data-path="high-throughput-experimental-methods-in-genomics.html"><a href="high-throughput-experimental-methods-in-genomics.html#the-general-idea-behind-high-throughput-techniques"><i class="fa fa-check"></i><b>1.4.1</b> The general idea behind high-throughput techniques</a></li>
<li class="chapter" data-level="1.4.2" data-path="high-throughput-experimental-methods-in-genomics.html"><a href="high-throughput-experimental-methods-in-genomics.html#high-throughput-sequencing"><i class="fa fa-check"></i><b>1.4.2</b> High-throughput sequencing</a></li>
</ul></li>
<li class="chapter" data-level="1.5" data-path="visualization-and-data-repositories-for-genomics.html"><a href="visualization-and-data-repositories-for-genomics.html"><i class="fa fa-check"></i><b>1.5</b> Visualization and data repositories for genomics</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="Rintro.html"><a href="Rintro.html"><i class="fa fa-check"></i><b>2</b> Introduction to R for Genomic Data Analysis</a><ul>
<li class="chapter" data-level="2.1" data-path="steps-of-genomic-data-analysis.html"><a href="steps-of-genomic-data-analysis.html"><i class="fa fa-check"></i><b>2.1</b> Steps of (genomic) data analysis</a><ul>
<li class="chapter" data-level="2.1.1" data-path="steps-of-genomic-data-analysis.html"><a href="steps-of-genomic-data-analysis.html#data-collection"><i class="fa fa-check"></i><b>2.1.1</b> Data collection</a></li>
<li class="chapter" data-level="2.1.2" data-path="steps-of-genomic-data-analysis.html"><a href="steps-of-genomic-data-analysis.html#data-quality-check-and-cleaning"><i class="fa fa-check"></i><b>2.1.2</b> Data quality check and cleaning</a></li>
<li class="chapter" data-level="2.1.3" data-path="steps-of-genomic-data-analysis.html"><a href="steps-of-genomic-data-analysis.html#data-processing"><i class="fa fa-check"></i><b>2.1.3</b> Data processing</a></li>
<li class="chapter" data-level="2.1.4" data-path="steps-of-genomic-data-analysis.html"><a href="steps-of-genomic-data-analysis.html#exploratory-data-analysis-and-modeling"><i class="fa fa-check"></i><b>2.1.4</b> Exploratory data analysis and modeling</a></li>
<li class="chapter" data-level="2.1.5" data-path="steps-of-genomic-data-analysis.html"><a href="steps-of-genomic-data-analysis.html#visualization-and-reporting"><i class="fa fa-check"></i><b>2.1.5</b> Visualization and reporting</a></li>
<li class="chapter" data-level="2.1.6" data-path="steps-of-genomic-data-analysis.html"><a href="steps-of-genomic-data-analysis.html#why-use-r-for-genomics"><i class="fa fa-check"></i><b>2.1.6</b> Why use R for genomics ?</a></li>
</ul></li>
<li class="chapter" data-level="2.2" data-path="getting-started-with-r.html"><a href="getting-started-with-r.html"><i class="fa fa-check"></i><b>2.2</b> Getting started with R</a><ul>
<li class="chapter" data-level="2.2.1" data-path="getting-started-with-r.html"><a href="getting-started-with-r.html#installing-packages"><i class="fa fa-check"></i><b>2.2.1</b> Installing packages</a></li>
<li class="chapter" data-level="2.2.2" data-path="getting-started-with-r.html"><a href="getting-started-with-r.html#installing-packages-in-custom-locations"><i class="fa fa-check"></i><b>2.2.2</b> Installing packages in custom locations</a></li>
<li class="chapter" data-level="2.2.3" data-path="getting-started-with-r.html"><a href="getting-started-with-r.html#getting-help-on-functions-and-packages"><i class="fa fa-check"></i><b>2.2.3</b> Getting help on functions and packages</a></li>
</ul></li>
<li class="chapter" data-level="2.3" data-path="computations-in-r.html"><a href="computations-in-r.html"><i class="fa fa-check"></i><b>2.3</b> Computations in R</a></li>
<li class="chapter" data-level="2.4" data-path="data-structures.html"><a href="data-structures.html"><i class="fa fa-check"></i><b>2.4</b> Data structures</a><ul>
<li class="chapter" data-level="2.4.1" data-path="data-structures.html"><a href="data-structures.html#vectors"><i class="fa fa-check"></i><b>2.4.1</b> Vectors</a></li>
<li class="chapter" data-level="2.4.2" data-path="data-structures.html"><a href="data-structures.html#matrices"><i class="fa fa-check"></i><b>2.4.2</b> Matrices</a></li>
<li class="chapter" data-level="2.4.3" data-path="data-structures.html"><a href="data-structures.html#data-frames"><i class="fa fa-check"></i><b>2.4.3</b> Data frames</a></li>
<li class="chapter" data-level="2.4.4" data-path="data-structures.html"><a href="data-structures.html#lists"><i class="fa fa-check"></i><b>2.4.4</b> Lists</a></li>
<li class="chapter" data-level="2.4.5" data-path="data-structures.html"><a href="data-structures.html#factors"><i class="fa fa-check"></i><b>2.4.5</b> Factors</a></li>
</ul></li>
<li class="chapter" data-level="2.5" data-path="data-types.html"><a href="data-types.html"><i class="fa fa-check"></i><b>2.5</b> Data types</a></li>
<li class="chapter" data-level="2.6" data-path="reading-and-writing-data.html"><a href="reading-and-writing-data.html"><i class="fa fa-check"></i><b>2.6</b> Reading and writing data</a><ul>
<li class="chapter" data-level="2.6.1" data-path="reading-and-writing-data.html"><a href="reading-and-writing-data.html#reading-large-files"><i class="fa fa-check"></i><b>2.6.1</b> Reading large files</a></li>
</ul></li>
<li class="chapter" data-level="2.7" data-path="plotting-in-r-with-base-graphics.html"><a href="plotting-in-r-with-base-graphics.html"><i class="fa fa-check"></i><b>2.7</b> Plotting in R with base graphics</a><ul>
<li class="chapter" data-level="2.7.1" data-path="plotting-in-r-with-base-graphics.html"><a href="plotting-in-r-with-base-graphics.html#combining-multiple-plots"><i class="fa fa-check"></i><b>2.7.1</b> Combining multiple plots</a></li>
<li class="chapter" data-level="2.7.2" data-path="plotting-in-r-with-base-graphics.html"><a href="plotting-in-r-with-base-graphics.html#saving-plots"><i class="fa fa-check"></i><b>2.7.2</b> Saving plots</a></li>
</ul></li>
<li class="chapter" data-level="2.8" data-path="plotting-in-r-with-ggplot2.html"><a href="plotting-in-r-with-ggplot2.html"><i class="fa fa-check"></i><b>2.8</b> Plotting in R with ggplot2</a><ul>
<li class="chapter" data-level="2.8.1" data-path="plotting-in-r-with-ggplot2.html"><a href="plotting-in-r-with-ggplot2.html#combining-multiple-plots-1"><i class="fa fa-check"></i><b>2.8.1</b> Combining multiple plots</a></li>
<li class="chapter" data-level="2.8.2" data-path="plotting-in-r-with-ggplot2.html"><a href="plotting-in-r-with-ggplot2.html#ggplot2-and-tidyverse"><i class="fa fa-check"></i><b>2.8.2</b> ggplot2 and tidyverse</a></li>
</ul></li>
<li class="chapter" data-level="2.9" data-path="functions-and-control-structures-for-ifelse-etc-.html"><a href="functions-and-control-structures-for-ifelse-etc-.html"><i class="fa fa-check"></i><b>2.9</b> Functions and control structures (for, if/else etc.)</a><ul>
<li class="chapter" data-level="2.9.1" data-path="functions-and-control-structures-for-ifelse-etc-.html"><a href="functions-and-control-structures-for-ifelse-etc-.html#user-defined-functions"><i class="fa fa-check"></i><b>2.9.1</b> User-defined functions</a></li>
<li class="chapter" data-level="2.9.2" data-path="functions-and-control-structures-for-ifelse-etc-.html"><a href="functions-and-control-structures-for-ifelse-etc-.html#loops-and-looping-structures-in-r"><i class="fa fa-check"></i><b>2.9.2</b> Loops and looping structures in R</a></li>
</ul></li>
<li class="chapter" data-level="2.10" data-path="exercises.html"><a href="exercises.html"><i class="fa fa-check"></i><b>2.10</b> Exercises</a><ul>
<li class="chapter" data-level="2.10.1" data-path="exercises.html"><a href="exercises.html#computations-in-r-1"><i class="fa fa-check"></i><b>2.10.1</b> Computations in R</a></li>
<li class="chapter" data-level="2.10.2" data-path="exercises.html"><a href="exercises.html#data-structures-in-r"><i class="fa fa-check"></i><b>2.10.2</b> Data structures in R</a></li>
<li class="chapter" data-level="2.10.3" data-path="exercises.html"><a href="exercises.html#reading-in-and-writing-data-out-in-r"><i class="fa fa-check"></i><b>2.10.3</b> Reading in and writing data out in R</a></li>
<li class="chapter" data-level="2.10.4" data-path="exercises.html"><a href="exercises.html#plotting-in-r"><i class="fa fa-check"></i><b>2.10.4</b> Plotting in R</a></li>
<li class="chapter" data-level="2.10.5" data-path="exercises.html"><a href="exercises.html#functions-and-control-structures-for-ifelse-etc.-1"><i class="fa fa-check"></i><b>2.10.5</b> Functions and control structures (for, if/else, etc.)</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="3" data-path="stats.html"><a href="stats.html"><i class="fa fa-check"></i><b>3</b> Statistics for Genomics</a><ul>
<li class="chapter" data-level="3.1" data-path="how-to-summarize-collection-of-data-points-the-idea-behind-statistical-distributions.html"><a href="how-to-summarize-collection-of-data-points-the-idea-behind-statistical-distributions.html"><i class="fa fa-check"></i><b>3.1</b> How to summarize collection of data points: The idea behind statistical distributions</a><ul>
<li class="chapter" data-level="3.1.1" data-path="how-to-summarize-collection-of-data-points-the-idea-behind-statistical-distributions.html"><a href="how-to-summarize-collection-of-data-points-the-idea-behind-statistical-distributions.html#describing-the-central-tendency-mean-and-median"><i class="fa fa-check"></i><b>3.1.1</b> Describing the central tendency: Mean and median</a></li>
<li class="chapter" data-level="3.1.2" data-path="how-to-summarize-collection-of-data-points-the-idea-behind-statistical-distributions.html"><a href="how-to-summarize-collection-of-data-points-the-idea-behind-statistical-distributions.html#describing-the-spread-measurements-of-variation"><i class="fa fa-check"></i><b>3.1.2</b> Describing the spread: Measurements of variation</a></li>
<li class="chapter" data-level="3.1.3" data-path="how-to-summarize-collection-of-data-points-the-idea-behind-statistical-distributions.html"><a href="how-to-summarize-collection-of-data-points-the-idea-behind-statistical-distributions.html#precision-of-estimates-confidence-intervals"><i class="fa fa-check"></i><b>3.1.3</b> Precision of estimates: Confidence intervals</a></li>
</ul></li>
<li class="chapter" data-level="3.2" data-path="how-to-test-for-differences-between-samples.html"><a href="how-to-test-for-differences-between-samples.html"><i class="fa fa-check"></i><b>3.2</b> How to test for differences between samples</a><ul>
<li class="chapter" data-level="3.2.1" data-path="how-to-test-for-differences-between-samples.html"><a href="how-to-test-for-differences-between-samples.html#randomization-based-testing-for-difference-of-the-means"><i class="fa fa-check"></i><b>3.2.1</b> Randomization-based testing for difference of the means</a></li>
<li class="chapter" data-level="3.2.2" data-path="how-to-test-for-differences-between-samples.html"><a href="how-to-test-for-differences-between-samples.html#using-t-test-for-difference-of-the-means-between-two-samples"><i class="fa fa-check"></i><b>3.2.2</b> Using t-test for difference of the means between two samples</a></li>
<li class="chapter" data-level="3.2.3" data-path="how-to-test-for-differences-between-samples.html"><a href="how-to-test-for-differences-between-samples.html#multiple-testing-correction"><i class="fa fa-check"></i><b>3.2.3</b> Multiple testing correction</a></li>
<li class="chapter" data-level="3.2.4" data-path="how-to-test-for-differences-between-samples.html"><a href="how-to-test-for-differences-between-samples.html#moderated-t-tests-using-information-from-multiple-comparisons"><i class="fa fa-check"></i><b>3.2.4</b> Moderated t-tests: Using information from multiple comparisons</a></li>
</ul></li>
<li class="chapter" data-level="3.3" data-path="relationship-between-variables-linear-models-and-correlation.html"><a href="relationship-between-variables-linear-models-and-correlation.html"><i class="fa fa-check"></i><b>3.3</b> Relationship between variables: Linear models and correlation</a><ul>
<li class="chapter" data-level="3.3.1" data-path="relationship-between-variables-linear-models-and-correlation.html"><a href="relationship-between-variables-linear-models-and-correlation.html#how-to-fit-a-line"><i class="fa fa-check"></i><b>3.3.1</b> How to fit a line</a></li>
<li class="chapter" data-level="3.3.2" data-path="relationship-between-variables-linear-models-and-correlation.html"><a href="relationship-between-variables-linear-models-and-correlation.html#how-to-estimate-the-error-of-the-coefficients"><i class="fa fa-check"></i><b>3.3.2</b> How to estimate the error of the coefficients</a></li>
<li class="chapter" data-level="3.3.3" data-path="relationship-between-variables-linear-models-and-correlation.html"><a href="relationship-between-variables-linear-models-and-correlation.html#accuracy-of-the-model"><i class="fa fa-check"></i><b>3.3.3</b> Accuracy of the model</a></li>
<li class="chapter" data-level="3.3.4" data-path="relationship-between-variables-linear-models-and-correlation.html"><a href="relationship-between-variables-linear-models-and-correlation.html#regression-with-categorical-variables"><i class="fa fa-check"></i><b>3.3.4</b> Regression with categorical variables</a></li>
<li class="chapter" data-level="3.3.5" data-path="relationship-between-variables-linear-models-and-correlation.html"><a href="relationship-between-variables-linear-models-and-correlation.html#regression-pitfalls"><i class="fa fa-check"></i><b>3.3.5</b> Regression pitfalls</a></li>
</ul></li>
<li class="chapter" data-level="3.4" data-path="exercises-1.html"><a href="exercises-1.html"><i class="fa fa-check"></i><b>3.4</b> Exercises</a><ul>
<li class="chapter" data-level="3.4.1" data-path="exercises-1.html"><a href="exercises-1.html#how-to-summarize-collection-of-data-points-the-idea-behind-statistical-distributions-1"><i class="fa fa-check"></i><b>3.4.1</b> How to summarize collection of data points: The idea behind statistical distributions</a></li>
<li class="chapter" data-level="3.4.2" data-path="exercises-1.html"><a href="exercises-1.html#how-to-test-for-differences-in-samples"><i class="fa fa-check"></i><b>3.4.2</b> How to test for differences in samples</a></li>
<li class="chapter" data-level="3.4.3" data-path="exercises-1.html"><a href="exercises-1.html#relationship-between-variables-linear-models-and-correlation-1"><i class="fa fa-check"></i><b>3.4.3</b> Relationship between variables: Linear models and correlation</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="4" data-path="unsupervisedLearning.html"><a href="unsupervisedLearning.html"><i class="fa fa-check"></i><b>4</b> Exploratory Data Analysis with Unsupervised Machine Learning</a><ul>
<li class="chapter" data-level="4.1" data-path="clustering-grouping-samples-based-on-their-similarity.html"><a href="clustering-grouping-samples-based-on-their-similarity.html"><i class="fa fa-check"></i><b>4.1</b> Clustering: Grouping samples based on their similarity</a><ul>
<li class="chapter" data-level="4.1.1" data-path="clustering-grouping-samples-based-on-their-similarity.html"><a href="clustering-grouping-samples-based-on-their-similarity.html#distance-metrics"><i class="fa fa-check"></i><b>4.1.1</b> Distance metrics</a></li>
<li class="chapter" data-level="4.1.2" data-path="clustering-grouping-samples-based-on-their-similarity.html"><a href="clustering-grouping-samples-based-on-their-similarity.html#hiearchical-clustering"><i class="fa fa-check"></i><b>4.1.2</b> Hiearchical clustering</a></li>
<li class="chapter" data-level="4.1.3" data-path="clustering-grouping-samples-based-on-their-similarity.html"><a href="clustering-grouping-samples-based-on-their-similarity.html#k-means-clustering"><i class="fa fa-check"></i><b>4.1.3</b> K-means clustering</a></li>
<li class="chapter" data-level="4.1.4" data-path="clustering-grouping-samples-based-on-their-similarity.html"><a href="clustering-grouping-samples-based-on-their-similarity.html#how-to-choose-k-the-number-of-clusters"><i class="fa fa-check"></i><b>4.1.4</b> How to choose “k”, the number of clusters</a></li>
</ul></li>
<li class="chapter" data-level="4.2" data-path="dimensionality-reduction-techniques-visualizing-complex-data-sets-in-2d.html"><a href="dimensionality-reduction-techniques-visualizing-complex-data-sets-in-2d.html"><i class="fa fa-check"></i><b>4.2</b> Dimensionality reduction techniques: Visualizing complex data sets in 2D</a><ul>
<li class="chapter" data-level="4.2.1" data-path="dimensionality-reduction-techniques-visualizing-complex-data-sets-in-2d.html"><a href="dimensionality-reduction-techniques-visualizing-complex-data-sets-in-2d.html#principal-component-analysis"><i class="fa fa-check"></i><b>4.2.1</b> Principal component analysis</a></li>
<li class="chapter" data-level="4.2.2" data-path="dimensionality-reduction-techniques-visualizing-complex-data-sets-in-2d.html"><a href="dimensionality-reduction-techniques-visualizing-complex-data-sets-in-2d.html#other-matrix-factorization-methods-for-dimensionality-reduction"><i class="fa fa-check"></i><b>4.2.2</b> Other matrix factorization methods for dimensionality reduction</a></li>
<li class="chapter" data-level="4.2.3" data-path="dimensionality-reduction-techniques-visualizing-complex-data-sets-in-2d.html"><a href="dimensionality-reduction-techniques-visualizing-complex-data-sets-in-2d.html#multi-dimensional-scaling"><i class="fa fa-check"></i><b>4.2.3</b> Multi-dimensional scaling</a></li>
<li class="chapter" data-level="4.2.4" data-path="dimensionality-reduction-techniques-visualizing-complex-data-sets-in-2d.html"><a href="dimensionality-reduction-techniques-visualizing-complex-data-sets-in-2d.html#t-distributed-stochastic-neighbor-embedding-t-sne"><i class="fa fa-check"></i><b>4.2.4</b> t-Distributed Stochastic Neighbor Embedding (t-SNE)</a></li>
</ul></li>
<li class="chapter" data-level="4.3" data-path="exercises-2.html"><a href="exercises-2.html"><i class="fa fa-check"></i><b>4.3</b> Exercises</a><ul>
<li class="chapter" data-level="4.3.1" data-path="exercises-2.html"><a href="exercises-2.html#clustering"><i class="fa fa-check"></i><b>4.3.1</b> Clustering</a></li>
<li class="chapter" data-level="4.3.2" data-path="exercises-2.html"><a href="exercises-2.html#dimension-reduction"><i class="fa fa-check"></i><b>4.3.2</b> Dimension reduction</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="5" data-path="supervisedLearning.html"><a href="supervisedLearning.html"><i class="fa fa-check"></i><b>5</b> Predictive Modeling with Supervised Machine Learning</a><ul>
<li class="chapter" data-level="5.1" data-path="how-are-machine-learning-models-fit.html"><a href="how-are-machine-learning-models-fit.html"><i class="fa fa-check"></i><b>5.1</b> How are machine learning models fit?</a><ul>
<li class="chapter" data-level="5.1.1" data-path="how-are-machine-learning-models-fit.html"><a href="how-are-machine-learning-models-fit.html#machine-learning-vs.-statistics"><i class="fa fa-check"></i><b>5.1.1</b> Machine learning vs. statistics</a></li>
</ul></li>
<li class="chapter" data-level="5.2" data-path="steps-in-supervised-machine-learning.html"><a href="steps-in-supervised-machine-learning.html"><i class="fa fa-check"></i><b>5.2</b> Steps in supervised machine learning</a></li>
<li class="chapter" data-level="5.3" data-path="use-case-disease-subtype-from-genomics-data.html"><a href="use-case-disease-subtype-from-genomics-data.html"><i class="fa fa-check"></i><b>5.3</b> Use case: Disease subtype from genomics data</a></li>
<li class="chapter" data-level="5.4" data-path="data-preprocessing.html"><a href="data-preprocessing.html"><i class="fa fa-check"></i><b>5.4</b> Data preprocessing</a><ul>
<li class="chapter" data-level="5.4.1" data-path="data-preprocessing.html"><a href="data-preprocessing.html#data-transformation"><i class="fa fa-check"></i><b>5.4.1</b> Data transformation</a></li>
<li class="chapter" data-level="5.4.2" data-path="data-preprocessing.html"><a href="data-preprocessing.html#filtering-data-and-scaling"><i class="fa fa-check"></i><b>5.4.2</b> Filtering data and scaling</a></li>
<li class="chapter" data-level="5.4.3" data-path="data-preprocessing.html"><a href="data-preprocessing.html#dealing-with-missing-values"><i class="fa fa-check"></i><b>5.4.3</b> Dealing with missing values</a></li>
</ul></li>
<li class="chapter" data-level="5.5" data-path="splitting-the-data.html"><a href="splitting-the-data.html"><i class="fa fa-check"></i><b>5.5</b> Splitting the data</a><ul>
<li class="chapter" data-level="5.5.1" data-path="splitting-the-data.html"><a href="splitting-the-data.html#holdout-test-dataset"><i class="fa fa-check"></i><b>5.5.1</b> Holdout test dataset</a></li>
<li class="chapter" data-level="5.5.2" data-path="splitting-the-data.html"><a href="splitting-the-data.html#cross-validation"><i class="fa fa-check"></i><b>5.5.2</b> Cross-validation</a></li>
<li class="chapter" data-level="5.5.3" data-path="splitting-the-data.html"><a href="splitting-the-data.html#bootstrap-resampling"><i class="fa fa-check"></i><b>5.5.3</b> Bootstrap resampling</a></li>
</ul></li>
<li class="chapter" data-level="5.6" data-path="predicting-the-subtype-with-k-nearest-neighbors.html"><a href="predicting-the-subtype-with-k-nearest-neighbors.html"><i class="fa fa-check"></i><b>5.6</b> Predicting the subtype with k-nearest neighbors</a></li>
<li class="chapter" data-level="5.7" data-path="assessing-the-performance-of-our-model.html"><a href="assessing-the-performance-of-our-model.html"><i class="fa fa-check"></i><b>5.7</b> Assessing the performance of our model</a><ul>
<li class="chapter" data-level="5.7.1" data-path="assessing-the-performance-of-our-model.html"><a href="assessing-the-performance-of-our-model.html#receiver-operating-characteristic-roc-curves"><i class="fa fa-check"></i><b>5.7.1</b> Receiver Operating Characteristic (ROC) curves</a></li>
</ul></li>
<li class="chapter" data-level="5.8" data-path="model-tuning-and-avoiding-overfitting.html"><a href="model-tuning-and-avoiding-overfitting.html"><i class="fa fa-check"></i><b>5.8</b> Model tuning and avoiding overfitting</a><ul>
<li class="chapter" data-level="5.8.1" data-path="model-tuning-and-avoiding-overfitting.html"><a href="model-tuning-and-avoiding-overfitting.html#model-complexity-and-bias-variance-trade-off"><i class="fa fa-check"></i><b>5.8.1</b> Model complexity and bias variance trade-off</a></li>
<li class="chapter" data-level="5.8.2" data-path="model-tuning-and-avoiding-overfitting.html"><a href="model-tuning-and-avoiding-overfitting.html#data-split-strategies-for-model-tuning-and-testing"><i class="fa fa-check"></i><b>5.8.2</b> Data split strategies for model tuning and testing</a></li>
</ul></li>
<li class="chapter" data-level="5.9" data-path="variable-importance.html"><a href="variable-importance.html"><i class="fa fa-check"></i><b>5.9</b> Variable importance</a></li>
<li class="chapter" data-level="5.10" data-path="how-to-deal-with-class-imbalance.html"><a href="how-to-deal-with-class-imbalance.html"><i class="fa fa-check"></i><b>5.10</b> How to deal with class imbalance</a><ul>
<li class="chapter" data-level="5.10.1" data-path="how-to-deal-with-class-imbalance.html"><a href="how-to-deal-with-class-imbalance.html#sampling-for-class-balance"><i class="fa fa-check"></i><b>5.10.1</b> Sampling for class balance</a></li>
<li class="chapter" data-level="5.10.2" data-path="how-to-deal-with-class-imbalance.html"><a href="how-to-deal-with-class-imbalance.html#altering-case-weights"><i class="fa fa-check"></i><b>5.10.2</b> Altering case weights</a></li>
<li class="chapter" data-level="5.10.3" data-path="how-to-deal-with-class-imbalance.html"><a href="how-to-deal-with-class-imbalance.html#selecting-different-classification-score-cutoffs"><i class="fa fa-check"></i><b>5.10.3</b> Selecting different classification score cutoffs</a></li>
</ul></li>
<li class="chapter" data-level="5.11" data-path="dealing-with-correlated-predictors.html"><a href="dealing-with-correlated-predictors.html"><i class="fa fa-check"></i><b>5.11</b> Dealing with correlated predictors</a></li>
<li class="chapter" data-level="5.12" data-path="trees-and-forests-random-forests-in-action.html"><a href="trees-and-forests-random-forests-in-action.html"><i class="fa fa-check"></i><b>5.12</b> Trees and forests: Random forests in action</a><ul>
<li class="chapter" data-level="5.12.1" data-path="trees-and-forests-random-forests-in-action.html"><a href="trees-and-forests-random-forests-in-action.html#decision-trees"><i class="fa fa-check"></i><b>5.12.1</b> Decision trees</a></li>
<li class="chapter" data-level="5.12.2" data-path="trees-and-forests-random-forests-in-action.html"><a href="trees-and-forests-random-forests-in-action.html#trees-to-forests"><i class="fa fa-check"></i><b>5.12.2</b> Trees to forests</a></li>
<li class="chapter" data-level="5.12.3" data-path="trees-and-forests-random-forests-in-action.html"><a href="trees-and-forests-random-forests-in-action.html#variable-importance-1"><i class="fa fa-check"></i><b>5.12.3</b> Variable importance</a></li>
</ul></li>
<li class="chapter" data-level="5.13" data-path="logistic-regression-and-regularization.html"><a href="logistic-regression-and-regularization.html"><i class="fa fa-check"></i><b>5.13</b> Logistic regression and regularization</a><ul>
<li class="chapter" data-level="5.13.1" data-path="logistic-regression-and-regularization.html"><a href="logistic-regression-and-regularization.html#regularization-in-order-to-avoid-overfitting"><i class="fa fa-check"></i><b>5.13.1</b> Regularization in order to avoid overfitting</a></li>
<li class="chapter" data-level="5.13.2" data-path="logistic-regression-and-regularization.html"><a href="logistic-regression-and-regularization.html#variable-importance-2"><i class="fa fa-check"></i><b>5.13.2</b> Variable importance</a></li>
</ul></li>
<li class="chapter" data-level="5.14" data-path="other-supervised-algorithms.html"><a href="other-supervised-algorithms.html"><i class="fa fa-check"></i><b>5.14</b> Other supervised algorithms</a><ul>
<li class="chapter" data-level="5.14.1" data-path="other-supervised-algorithms.html"><a href="other-supervised-algorithms.html#gradient-boosting"><i class="fa fa-check"></i><b>5.14.1</b> Gradient boosting</a></li>
<li class="chapter" data-level="5.14.2" data-path="other-supervised-algorithms.html"><a href="other-supervised-algorithms.html#support-vector-machines-svm"><i class="fa fa-check"></i><b>5.14.2</b> Support Vector Machines (SVM)</a></li>
<li class="chapter" data-level="5.14.3" data-path="other-supervised-algorithms.html"><a href="other-supervised-algorithms.html#neural-networks-and-deep-versions-of-it"><i class="fa fa-check"></i><b>5.14.3</b> Neural networks and deep versions of it</a></li>
<li class="chapter" data-level="5.14.4" data-path="other-supervised-algorithms.html"><a href="other-supervised-algorithms.html#ensemble-learning"><i class="fa fa-check"></i><b>5.14.4</b> Ensemble learning</a></li>
</ul></li>
<li class="chapter" data-level="5.15" data-path="predicting-continuous-variables-regression-with-machine-learning.html"><a href="predicting-continuous-variables-regression-with-machine-learning.html"><i class="fa fa-check"></i><b>5.15</b> Predicting continuous variables: Regression with machine learning</a><ul>
<li class="chapter" data-level="5.15.1" data-path="predicting-continuous-variables-regression-with-machine-learning.html"><a href="predicting-continuous-variables-regression-with-machine-learning.html#use-case-predicting-age-from-dna-methylation"><i class="fa fa-check"></i><b>5.15.1</b> Use case: Predicting age from DNA methylation</a></li>
<li class="chapter" data-level="5.15.2" data-path="predicting-continuous-variables-regression-with-machine-learning.html"><a href="predicting-continuous-variables-regression-with-machine-learning.html#reading-and-processing-the-data"><i class="fa fa-check"></i><b>5.15.2</b> Reading and processing the data</a></li>
<li class="chapter" data-level="5.15.3" data-path="predicting-continuous-variables-regression-with-machine-learning.html"><a href="predicting-continuous-variables-regression-with-machine-learning.html#running-random-forest-regression"><i class="fa fa-check"></i><b>5.15.3</b> Running random forest regression</a></li>
</ul></li>
<li class="chapter" data-level="5.16" data-path="exercises-3.html"><a href="exercises-3.html"><i class="fa fa-check"></i><b>5.16</b> Exercises</a><ul>
<li class="chapter" data-level="5.16.1" data-path="exercises-3.html"><a href="exercises-3.html#classification"><i class="fa fa-check"></i><b>5.16.1</b> Classification</a></li>
<li class="chapter" data-level="5.16.2" data-path="exercises-3.html"><a href="exercises-3.html#regression"><i class="fa fa-check"></i><b>5.16.2</b> Regression</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="6" data-path="genomicIntervals.html"><a href="genomicIntervals.html"><i class="fa fa-check"></i><b>6</b> Operations on Genomic Intervals and Genome Arithmetic</a><ul>
<li class="chapter" data-level="6.1" data-path="operations-on-genomic-intervals-with-genomicranges-package.html"><a href="operations-on-genomic-intervals-with-genomicranges-package.html"><i class="fa fa-check"></i><b>6.1</b> Operations on genomic intervals with <code>GenomicRanges</code> package</a><ul>
<li class="chapter" data-level="6.1.1" data-path="operations-on-genomic-intervals-with-genomicranges-package.html"><a href="operations-on-genomic-intervals-with-genomicranges-package.html#how-to-create-and-manipulate-a-granges-object"><i class="fa fa-check"></i><b>6.1.1</b> How to create and manipulate a GRanges object</a></li>
<li class="chapter" data-level="6.1.2" data-path="operations-on-genomic-intervals-with-genomicranges-package.html"><a href="operations-on-genomic-intervals-with-genomicranges-package.html#getting-genomic-regions-into-r-as-granges-objects"><i class="fa fa-check"></i><b>6.1.2</b> Getting genomic regions into R as GRanges objects</a></li>
<li class="chapter" data-level="6.1.3" data-path="operations-on-genomic-intervals-with-genomicranges-package.html"><a href="operations-on-genomic-intervals-with-genomicranges-package.html#finding-regions-that-dodo-not-overlap-with-another-set-of-regions"><i class="fa fa-check"></i><b>6.1.3</b> Finding regions that do/do not overlap with another set of regions</a></li>
</ul></li>
<li class="chapter" data-level="6.2" data-path="dealing-with-mapped-high-throughput-sequencing-reads.html"><a href="dealing-with-mapped-high-throughput-sequencing-reads.html"><i class="fa fa-check"></i><b>6.2</b> Dealing with mapped high-throughput sequencing reads</a><ul>
<li class="chapter" data-level="6.2.1" data-path="dealing-with-mapped-high-throughput-sequencing-reads.html"><a href="dealing-with-mapped-high-throughput-sequencing-reads.html#counting-mapped-reads-for-a-set-of-regions"><i class="fa fa-check"></i><b>6.2.1</b> Counting mapped reads for a set of regions</a></li>
</ul></li>
<li class="chapter" data-level="6.3" data-path="dealing-with-continuous-scores-over-the-genome.html"><a href="dealing-with-continuous-scores-over-the-genome.html"><i class="fa fa-check"></i><b>6.3</b> Dealing with continuous scores over the genome</a><ul>
<li class="chapter" data-level="6.3.1" data-path="dealing-with-continuous-scores-over-the-genome.html"><a href="dealing-with-continuous-scores-over-the-genome.html#extracting-subsections-of-rle-and-rlelist-objects"><i class="fa fa-check"></i><b>6.3.1</b> Extracting subsections of Rle and RleList objects</a></li>
</ul></li>
<li class="chapter" data-level="6.4" data-path="genomic-intervals-with-more-information-summarizedexperiment-class.html"><a href="genomic-intervals-with-more-information-summarizedexperiment-class.html"><i class="fa fa-check"></i><b>6.4</b> Genomic intervals with more information: SummarizedExperiment class</a><ul>
<li class="chapter" data-level="6.4.1" data-path="genomic-intervals-with-more-information-summarizedexperiment-class.html"><a href="genomic-intervals-with-more-information-summarizedexperiment-class.html#create-a-summarizedexperiment-object"><i class="fa fa-check"></i><b>6.4.1</b> Create a SummarizedExperiment object</a></li>
<li class="chapter" data-level="6.4.2" data-path="genomic-intervals-with-more-information-summarizedexperiment-class.html"><a href="genomic-intervals-with-more-information-summarizedexperiment-class.html#subset-and-manipulate-the-summarizedexperiment-object"><i class="fa fa-check"></i><b>6.4.2</b> Subset and manipulate the SummarizedExperiment object</a></li>
</ul></li>
<li class="chapter" data-level="6.5" data-path="visualizing-and-summarizing-genomic-intervals.html"><a href="visualizing-and-summarizing-genomic-intervals.html"><i class="fa fa-check"></i><b>6.5</b> Visualizing and summarizing genomic intervals</a><ul>
<li class="chapter" data-level="6.5.1" data-path="visualizing-and-summarizing-genomic-intervals.html"><a href="visualizing-and-summarizing-genomic-intervals.html#visualizing-intervals-on-a-locus-of-interest"><i class="fa fa-check"></i><b>6.5.1</b> Visualizing intervals on a locus of interest</a></li>
<li class="chapter" data-level="6.5.2" data-path="visualizing-and-summarizing-genomic-intervals.html"><a href="visualizing-and-summarizing-genomic-intervals.html#summaries-of-genomic-intervals-on-multiple-loci"><i class="fa fa-check"></i><b>6.5.2</b> Summaries of genomic intervals on multiple loci</a></li>
<li class="chapter" data-level="6.5.3" data-path="visualizing-and-summarizing-genomic-intervals.html"><a href="visualizing-and-summarizing-genomic-intervals.html#making-karyograms-and-circos-plots"><i class="fa fa-check"></i><b>6.5.3</b> Making karyograms and circos plots</a></li>
</ul></li>
<li class="chapter" data-level="6.6" data-path="exercises-4.html"><a href="exercises-4.html"><i class="fa fa-check"></i><b>6.6</b> Exercises</a><ul>
<li class="chapter" data-level="6.6.1" data-path="exercises-4.html"><a href="exercises-4.html#operations-on-genomic-intervals-with-the-genomicranges-package"><i class="fa fa-check"></i><b>6.6.1</b> Operations on genomic intervals with the <code>GenomicRanges</code> package</a></li>
<li class="chapter" data-level="6.6.2" data-path="exercises-4.html"><a href="exercises-4.html#dealing-with-mapped-high-throughput-sequencing-reads-1"><i class="fa fa-check"></i><b>6.6.2</b> Dealing with mapped high-throughput sequencing reads</a></li>
<li class="chapter" data-level="6.6.3" data-path="exercises-4.html"><a href="exercises-4.html#dealing-with-contiguous-scores-over-the-genome"><i class="fa fa-check"></i><b>6.6.3</b> Dealing with contiguous scores over the genome</a></li>
<li class="chapter" data-level="6.6.4" data-path="exercises-4.html"><a href="exercises-4.html#visualizing-and-summarizing-genomic-intervals-1"><i class="fa fa-check"></i><b>6.6.4</b> Visualizing and summarizing genomic intervals</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="7" data-path="processingReads.html"><a href="processingReads.html"><i class="fa fa-check"></i><b>7</b> Quality Check, Processing and Alignment of High-throughput Sequencing Reads</a><ul>
<li class="chapter" data-level="7.1" data-path="fasta-and-fastq-formats.html"><a href="fasta-and-fastq-formats.html"><i class="fa fa-check"></i><b>7.1</b> FASTA and FASTQ formats</a></li>
<li class="chapter" data-level="7.2" data-path="quality-check-on-sequencing-reads.html"><a href="quality-check-on-sequencing-reads.html"><i class="fa fa-check"></i><b>7.2</b> Quality check on sequencing reads</a><ul>
<li class="chapter" data-level="7.2.1" data-path="quality-check-on-sequencing-reads.html"><a href="quality-check-on-sequencing-reads.html#sequence-quality-per-basecycle"><i class="fa fa-check"></i><b>7.2.1</b> Sequence quality per base/cycle</a></li>
<li class="chapter" data-level="7.2.2" data-path="quality-check-on-sequencing-reads.html"><a href="quality-check-on-sequencing-reads.html#sequence-content-per-basecycle"><i class="fa fa-check"></i><b>7.2.2</b> Sequence content per base/cycle</a></li>
<li class="chapter" data-level="7.2.3" data-path="quality-check-on-sequencing-reads.html"><a href="quality-check-on-sequencing-reads.html#read-frequency-plot"><i class="fa fa-check"></i><b>7.2.3</b> Read frequency plot</a></li>
<li class="chapter" data-level="7.2.4" data-path="quality-check-on-sequencing-reads.html"><a href="quality-check-on-sequencing-reads.html#other-quality-metrics-and-qc-tools"><i class="fa fa-check"></i><b>7.2.4</b> Other quality metrics and QC tools</a></li>
</ul></li>
<li class="chapter" data-level="7.3" data-path="filtering-and-trimming-reads.html"><a href="filtering-and-trimming-reads.html"><i class="fa fa-check"></i><b>7.3</b> Filtering and trimming reads</a></li>
<li class="chapter" data-level="7.4" data-path="mappingaligning-reads-to-the-genome.html"><a href="mappingaligning-reads-to-the-genome.html"><i class="fa fa-check"></i><b>7.4</b> Mapping/aligning reads to the genome</a></li>
<li class="chapter" data-level="7.5" data-path="further-processing-of-aligned-reads.html"><a href="further-processing-of-aligned-reads.html"><i class="fa fa-check"></i><b>7.5</b> Further processing of aligned reads</a></li>
<li class="chapter" data-level="7.6" data-path="exercises-5.html"><a href="exercises-5.html"><i class="fa fa-check"></i><b>7.6</b> Exercises</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="rnaseqanalysis.html"><a href="rnaseqanalysis.html"><i class="fa fa-check"></i><b>8</b> RNA-seq Analysis</a><ul>
<li class="chapter" data-level="8.1" data-path="what-is-gene-expression.html"><a href="what-is-gene-expression.html"><i class="fa fa-check"></i><b>8.1</b> What is gene expression?</a></li>
<li class="chapter" data-level="8.2" data-path="methods-to-detect-gene-expression.html"><a href="methods-to-detect-gene-expression.html"><i class="fa fa-check"></i><b>8.2</b> Methods to detect gene expression</a></li>
<li class="chapter" data-level="8.3" data-path="gene-expression-analysis-using-high-throughput-sequencing-technologies.html"><a href="gene-expression-analysis-using-high-throughput-sequencing-technologies.html"><i class="fa fa-check"></i><b>8.3</b> Gene expression analysis using high-throughput sequencing technologies</a><ul>
<li class="chapter" data-level="8.3.1" data-path="gene-expression-analysis-using-high-throughput-sequencing-technologies.html"><a href="gene-expression-analysis-using-high-throughput-sequencing-technologies.html#processing-raw-data"><i class="fa fa-check"></i><b>8.3.1</b> Processing raw data</a></li>
<li class="chapter" data-level="8.3.2" data-path="gene-expression-analysis-using-high-throughput-sequencing-technologies.html"><a href="gene-expression-analysis-using-high-throughput-sequencing-technologies.html#alignment"><i class="fa fa-check"></i><b>8.3.2</b> Alignment</a></li>
<li class="chapter" data-level="8.3.3" data-path="gene-expression-analysis-using-high-throughput-sequencing-technologies.html"><a href="gene-expression-analysis-using-high-throughput-sequencing-technologies.html#quantification"><i class="fa fa-check"></i><b>8.3.3</b> Quantification</a></li>
<li class="chapter" data-level="8.3.4" data-path="gene-expression-analysis-using-high-throughput-sequencing-technologies.html"><a href="gene-expression-analysis-using-high-throughput-sequencing-technologies.html#within-sample-normalization-of-the-read-counts"><i class="fa fa-check"></i><b>8.3.4</b> Within sample normalization of the read counts</a></li>
<li class="chapter" data-level="8.3.5" data-path="gene-expression-analysis-using-high-throughput-sequencing-technologies.html"><a href="gene-expression-analysis-using-high-throughput-sequencing-technologies.html#computing-different-normalization-schemes-in-r"><i class="fa fa-check"></i><b>8.3.5</b> Computing different normalization schemes in R</a></li>
<li class="chapter" data-level="8.3.6" data-path="gene-expression-analysis-using-high-throughput-sequencing-technologies.html"><a href="gene-expression-analysis-using-high-throughput-sequencing-technologies.html#exploratory-analysis-of-the-read-count-table"><i class="fa fa-check"></i><b>8.3.6</b> Exploratory analysis of the read count table</a></li>
<li class="chapter" data-level="8.3.7" data-path="gene-expression-analysis-using-high-throughput-sequencing-technologies.html"><a href="gene-expression-analysis-using-high-throughput-sequencing-technologies.html#differential-expression-analysis"><i class="fa fa-check"></i><b>8.3.7</b> Differential expression analysis</a></li>
<li class="chapter" data-level="8.3.8" data-path="gene-expression-analysis-using-high-throughput-sequencing-technologies.html"><a href="gene-expression-analysis-using-high-throughput-sequencing-technologies.html#functional-enrichment-analysis"><i class="fa fa-check"></i><b>8.3.8</b> Functional enrichment analysis</a></li>
<li class="chapter" data-level="8.3.9" data-path="gene-expression-analysis-using-high-throughput-sequencing-technologies.html"><a href="gene-expression-analysis-using-high-throughput-sequencing-technologies.html#accounting-for-additional-sources-of-variation"><i class="fa fa-check"></i><b>8.3.9</b> Accounting for additional sources of variation</a></li>
</ul></li>
<li class="chapter" data-level="8.4" data-path="other-applications-of-rna-seq.html"><a href="other-applications-of-rna-seq.html"><i class="fa fa-check"></i><b>8.4</b> Other applications of RNA-seq</a></li>
<li class="chapter" data-level="8.5" data-path="exercises-6.html"><a href="exercises-6.html"><i class="fa fa-check"></i><b>8.5</b> Exercises</a><ul>
<li class="chapter" data-level="8.5.1" data-path="exercises-6.html"><a href="exercises-6.html#exploring-the-count-tables"><i class="fa fa-check"></i><b>8.5.1</b> Exploring the count tables</a></li>
<li class="chapter" data-level="8.5.2" data-path="exercises-6.html"><a href="exercises-6.html#differential-expression-analysis-1"><i class="fa fa-check"></i><b>8.5.2</b> Differential expression analysis</a></li>
<li class="chapter" data-level="8.5.3" data-path="exercises-6.html"><a href="exercises-6.html#functional-enrichment-analysis-1"><i class="fa fa-check"></i><b>8.5.3</b> Functional enrichment analysis</a></li>
<li class="chapter" data-level="8.5.4" data-path="exercises-6.html"><a href="exercises-6.html#removing-unwanted-variation-from-the-expression-data"><i class="fa fa-check"></i><b>8.5.4</b> Removing unwanted variation from the expression data</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="9" data-path="chipseq.html"><a href="chipseq.html"><i class="fa fa-check"></i><b>9</b> ChIP-seq analysis</a><ul>
<li class="chapter" data-level="9.1" data-path="regulatory-protein-dna-interactions.html"><a href="regulatory-protein-dna-interactions.html"><i class="fa fa-check"></i><b>9.1</b> Regulatory protein-DNA interactions</a></li>
<li class="chapter" data-level="9.2" data-path="measuring-protein-dna-interactions-with-chip-seq.html"><a href="measuring-protein-dna-interactions-with-chip-seq.html"><i class="fa fa-check"></i><b>9.2</b> Measuring protein-DNA interactions with ChIP-seq</a></li>
<li class="chapter" data-level="9.3" data-path="factors-that-affect-chip-seq-experiment-and-analysis-quality.html"><a href="factors-that-affect-chip-seq-experiment-and-analysis-quality.html"><i class="fa fa-check"></i><b>9.3</b> Factors that affect ChIP-seq experiment and analysis quality</a><ul>
<li class="chapter" data-level="9.3.1" data-path="factors-that-affect-chip-seq-experiment-and-analysis-quality.html"><a href="factors-that-affect-chip-seq-experiment-and-analysis-quality.html#antibody-specificity"><i class="fa fa-check"></i><b>9.3.1</b> Antibody specificity</a></li>
<li class="chapter" data-level="9.3.2" data-path="factors-that-affect-chip-seq-experiment-and-analysis-quality.html"><a href="factors-that-affect-chip-seq-experiment-and-analysis-quality.html#sequencing-depth"><i class="fa fa-check"></i><b>9.3.2</b> Sequencing depth</a></li>
<li class="chapter" data-level="9.3.3" data-path="factors-that-affect-chip-seq-experiment-and-analysis-quality.html"><a href="factors-that-affect-chip-seq-experiment-and-analysis-quality.html#pcr-duplication"><i class="fa fa-check"></i><b>9.3.3</b> PCR duplication</a></li>
<li class="chapter" data-level="9.3.4" data-path="factors-that-affect-chip-seq-experiment-and-analysis-quality.html"><a href="factors-that-affect-chip-seq-experiment-and-analysis-quality.html#biological-replicates"><i class="fa fa-check"></i><b>9.3.4</b> Biological replicates</a></li>
<li class="chapter" data-level="9.3.5" data-path="factors-that-affect-chip-seq-experiment-and-analysis-quality.html"><a href="factors-that-affect-chip-seq-experiment-and-analysis-quality.html#control-experiments"><i class="fa fa-check"></i><b>9.3.5</b> Control experiments</a></li>
<li class="chapter" data-level="9.3.6" data-path="factors-that-affect-chip-seq-experiment-and-analysis-quality.html"><a href="factors-that-affect-chip-seq-experiment-and-analysis-quality.html#using-tagged-proteins"><i class="fa fa-check"></i><b>9.3.6</b> Using tagged proteins</a></li>
</ul></li>
<li class="chapter" data-level="9.4" data-path="pre-processing-chip-data.html"><a href="pre-processing-chip-data.html"><i class="fa fa-check"></i><b>9.4</b> Pre-processing ChIP data</a><ul>
<li class="chapter" data-level="9.4.1" data-path="pre-processing-chip-data.html"><a href="pre-processing-chip-data.html#mapping-of-chip-seq-data"><i class="fa fa-check"></i><b>9.4.1</b> Mapping of ChIP-seq data</a></li>
</ul></li>
<li class="chapter" data-level="9.5" data-path="chip-quality-control.html"><a href="chip-quality-control.html"><i class="fa fa-check"></i><b>9.5</b> ChIP quality control</a><ul>
<li class="chapter" data-level="9.5.1" data-path="chip-quality-control.html"><a href="chip-quality-control.html#the-data"><i class="fa fa-check"></i><b>9.5.1</b> The data</a></li>
<li class="chapter" data-level="9.5.2" data-path="chip-quality-control.html"><a href="chip-quality-control.html#sample-clustering"><i class="fa fa-check"></i><b>9.5.2</b> Sample clustering</a></li>
<li class="chapter" data-level="9.5.3" data-path="chip-quality-control.html"><a href="chip-quality-control.html#visualization-in-the-genome-browser"><i class="fa fa-check"></i><b>9.5.3</b> Visualization in the genome browser</a></li>
<li class="chapter" data-level="9.5.4" data-path="chip-quality-control.html"><a href="chip-quality-control.html#plus-and-minus-strand-cross-correlation"><i class="fa fa-check"></i><b>9.5.4</b> Plus and minus strand cross-correlation</a></li>
<li class="chapter" data-level="9.5.5" data-path="chip-quality-control.html"><a href="chip-quality-control.html#gc-bias-quantification"><i class="fa fa-check"></i><b>9.5.5</b> GC bias quantification</a></li>
<li class="chapter" data-level="9.5.6" data-path="chip-quality-control.html"><a href="chip-quality-control.html#sequence-read-genomic-distribution"><i class="fa fa-check"></i><b>9.5.6</b> Sequence read genomic distribution</a></li>
</ul></li>
<li class="chapter" data-level="9.6" data-path="peak-calling.html"><a href="peak-calling.html"><i class="fa fa-check"></i><b>9.6</b> Peak calling</a><ul>
<li class="chapter" data-level="9.6.1" data-path="peak-calling.html"><a href="peak-calling.html#types-of-chip-seq-experiments"><i class="fa fa-check"></i><b>9.6.1</b> Types of ChIP-seq experiments</a></li>
<li class="chapter" data-level="9.6.2" data-path="peak-calling.html"><a href="peak-calling.html#peak-calling-sharp-peaks"><i class="fa fa-check"></i><b>9.6.2</b> Peak calling: Sharp peaks</a></li>
<li class="chapter" data-level="9.6.3" data-path="peak-calling.html"><a href="peak-calling.html#peak-calling-broad-regions"><i class="fa fa-check"></i><b>9.6.3</b> Peak calling: Broad regions</a></li>
<li class="chapter" data-level="9.6.4" data-path="peak-calling.html"><a href="peak-calling.html#peak-quality-control"><i class="fa fa-check"></i><b>9.6.4</b> Peak quality control</a></li>
<li class="chapter" data-level="9.6.5" data-path="peak-calling.html"><a href="peak-calling.html#peak-annotation"><i class="fa fa-check"></i><b>9.6.5</b> Peak annotation</a></li>
</ul></li>
<li class="chapter" data-level="9.7" data-path="motif-discovery.html"><a href="motif-discovery.html"><i class="fa fa-check"></i><b>9.7</b> Motif discovery</a><ul>
<li class="chapter" data-level="9.7.1" data-path="motif-discovery.html"><a href="motif-discovery.html#motif-comparison"><i class="fa fa-check"></i><b>9.7.1</b> Motif comparison</a></li>
</ul></li>
<li class="chapter" data-level="9.8" data-path="what-to-do-next.html"><a href="what-to-do-next.html"><i class="fa fa-check"></i><b>9.8</b> What to do next?</a></li>
<li class="chapter" data-level="9.9" data-path="exercises-7.html"><a href="exercises-7.html"><i class="fa fa-check"></i><b>9.9</b> Exercises</a><ul>
<li class="chapter" data-level="9.9.1" data-path="exercises-7.html"><a href="exercises-7.html#quality-control"><i class="fa fa-check"></i><b>9.9.1</b> Quality control</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="10" data-path="bsseq.html"><a href="bsseq.html"><i class="fa fa-check"></i><b>10</b> DNA methylation analysis using bisulfite sequencing data</a><ul>
<li class="chapter" data-level="10.1" data-path="what-is-dna-methylation.html"><a href="what-is-dna-methylation.html"><i class="fa fa-check"></i><b>10.1</b> What is DNA methylation?</a><ul>
<li class="chapter" data-level="10.1.1" data-path="what-is-dna-methylation.html"><a href="what-is-dna-methylation.html#how-dna-methylation-is-set"><i class="fa fa-check"></i><b>10.1.1</b> How DNA methylation is set ?</a></li>
<li class="chapter" data-level="10.1.2" data-path="what-is-dna-methylation.html"><a href="what-is-dna-methylation.html#how-to-measure-dna-methylation-with-bisulfite-sequencing"><i class="fa fa-check"></i><b>10.1.2</b> How to measure DNA methylation with bisulfite sequencing</a></li>
</ul></li>
<li class="chapter" data-level="10.2" data-path="analyzing-dna-methylation-data.html"><a href="analyzing-dna-methylation-data.html"><i class="fa fa-check"></i><b>10.2</b> Analyzing DNA methylation data</a></li>
<li class="chapter" data-level="10.3" data-path="processing-raw-data-and-getting-data-into-r.html"><a href="processing-raw-data-and-getting-data-into-r.html"><i class="fa fa-check"></i><b>10.3</b> Processing raw data and getting data into R</a></li>
<li class="chapter" data-level="10.4" data-path="data-filtering-and-exploratory-analysis.html"><a href="data-filtering-and-exploratory-analysis.html"><i class="fa fa-check"></i><b>10.4</b> Data filtering and exploratory analysis</a><ul>
<li class="chapter" data-level="10.4.1" data-path="data-filtering-and-exploratory-analysis.html"><a href="data-filtering-and-exploratory-analysis.html#reading-methylation-call-files"><i class="fa fa-check"></i><b>10.4.1</b> Reading methylation call files</a></li>
<li class="chapter" data-level="10.4.2" data-path="data-filtering-and-exploratory-analysis.html"><a href="data-filtering-and-exploratory-analysis.html#further-quality-check"><i class="fa fa-check"></i><b>10.4.2</b> Further quality check</a></li>
<li class="chapter" data-level="10.4.3" data-path="data-filtering-and-exploratory-analysis.html"><a href="data-filtering-and-exploratory-analysis.html#merging-samples-into-a-single-table"><i class="fa fa-check"></i><b>10.4.3</b> Merging samples into a single table</a></li>
<li class="chapter" data-level="10.4.4" data-path="data-filtering-and-exploratory-analysis.html"><a href="data-filtering-and-exploratory-analysis.html#filtering-cpgs"><i class="fa fa-check"></i><b>10.4.4</b> Filtering CpGs</a></li>
<li class="chapter" data-level="10.4.5" data-path="data-filtering-and-exploratory-analysis.html"><a href="data-filtering-and-exploratory-analysis.html#clustering-samples"><i class="fa fa-check"></i><b>10.4.5</b> Clustering samples</a></li>
<li class="chapter" data-level="10.4.6" data-path="data-filtering-and-exploratory-analysis.html"><a href="data-filtering-and-exploratory-analysis.html#principal-component-analysis-1"><i class="fa fa-check"></i><b>10.4.6</b> Principal component analysis</a></li>
</ul></li>
<li class="chapter" data-level="10.5" data-path="extracting-interesting-regions-differential-methylation-and-segmentation.html"><a href="extracting-interesting-regions-differential-methylation-and-segmentation.html"><i class="fa fa-check"></i><b>10.5</b> Extracting interesting regions: Differential methylation and segmentation</a><ul>
<li class="chapter" data-level="10.5.1" data-path="extracting-interesting-regions-differential-methylation-and-segmentation.html"><a href="extracting-interesting-regions-differential-methylation-and-segmentation.html#differential-methylation"><i class="fa fa-check"></i><b>10.5.1</b> Differential methylation</a></li>
<li class="chapter" data-level="10.5.2" data-path="extracting-interesting-regions-differential-methylation-and-segmentation.html"><a href="extracting-interesting-regions-differential-methylation-and-segmentation.html#methylation-segmentation"><i class="fa fa-check"></i><b>10.5.2</b> Methylation segmentation</a></li>
<li class="chapter" data-level="10.5.3" data-path="extracting-interesting-regions-differential-methylation-and-segmentation.html"><a href="extracting-interesting-regions-differential-methylation-and-segmentation.html#working-with-large-files"><i class="fa fa-check"></i><b>10.5.3</b> Working with large files</a></li>
</ul></li>
<li class="chapter" data-level="10.6" data-path="annotation-of-dmrsdmcs-and-segments.html"><a href="annotation-of-dmrsdmcs-and-segments.html"><i class="fa fa-check"></i><b>10.6</b> Annotation of DMRs/DMCs and segments</a><ul>
<li class="chapter" data-level="10.6.1" data-path="annotation-of-dmrsdmcs-and-segments.html"><a href="annotation-of-dmrsdmcs-and-segments.html#further-annotation-with-genes-or-gene-sets"><i class="fa fa-check"></i><b>10.6.1</b> Further annotation with genes or gene sets</a></li>
</ul></li>
<li class="chapter" data-level="10.7" data-path="other-r-packages-that-can-be-used-for-methylation-analysis.html"><a href="other-r-packages-that-can-be-used-for-methylation-analysis.html"><i class="fa fa-check"></i><b>10.7</b> Other R packages that can be used for methylation analysis</a></li>
<li class="chapter" data-level="10.8" data-path="exercises-8.html"><a href="exercises-8.html"><i class="fa fa-check"></i><b>10.8</b> Exercises</a><ul>
<li class="chapter" data-level="10.8.1" data-path="exercises-8.html"><a href="exercises-8.html#differential-methylation-1"><i class="fa fa-check"></i><b>10.8.1</b> Differential methylation</a></li>
<li class="chapter" data-level="10.8.2" data-path="exercises-8.html"><a href="exercises-8.html#methylome-segmentation"><i class="fa fa-check"></i><b>10.8.2</b> Methylome segmentation</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="11" data-path="multiomics.html"><a href="multiomics.html"><i class="fa fa-check"></i><b>11</b> Multi-omics Analysis</a><ul>
<li class="chapter" data-level="11.1" data-path="use-case-multi-omics-data-from-colorectal-cancer.html"><a href="use-case-multi-omics-data-from-colorectal-cancer.html"><i class="fa fa-check"></i><b>11.1</b> Use case: Multi-omics data from colorectal cancer</a></li>
<li class="chapter" data-level="11.2" data-path="latent-variable-models-for-multi-omics-integration.html"><a href="latent-variable-models-for-multi-omics-integration.html"><i class="fa fa-check"></i><b>11.2</b> Latent variable models for multi-omics integration</a></li>
<li class="chapter" data-level="11.3" data-path="matrix-factorization-methods-for-unsupervised-multi-omics-data-integration.html"><a href="matrix-factorization-methods-for-unsupervised-multi-omics-data-integration.html"><i class="fa fa-check"></i><b>11.3</b> Matrix factorization methods for unsupervised multi-omics data integration</a><ul>
<li class="chapter" data-level="11.3.1" data-path="matrix-factorization-methods-for-unsupervised-multi-omics-data-integration.html"><a href="matrix-factorization-methods-for-unsupervised-multi-omics-data-integration.html#multiple-factor-analysis"><i class="fa fa-check"></i><b>11.3.1</b> Multiple factor analysis</a></li>
<li class="chapter" data-level="11.3.2" data-path="matrix-factorization-methods-for-unsupervised-multi-omics-data-integration.html"><a href="matrix-factorization-methods-for-unsupervised-multi-omics-data-integration.html#joint-non-negative-matrix-factorization"><i class="fa fa-check"></i><b>11.3.2</b> Joint non-negative matrix factorization</a></li>
<li class="chapter" data-level="11.3.3" data-path="matrix-factorization-methods-for-unsupervised-multi-omics-data-integration.html"><a href="matrix-factorization-methods-for-unsupervised-multi-omics-data-integration.html#icluster"><i class="fa fa-check"></i><b>11.3.3</b> iCluster</a></li>
</ul></li>
<li class="chapter" data-level="11.4" data-path="clustering-using-latent-factors.html"><a href="clustering-using-latent-factors.html"><i class="fa fa-check"></i><b>11.4</b> Clustering using latent factors</a><ul>
<li class="chapter" data-level="11.4.1" data-path="clustering-using-latent-factors.html"><a href="clustering-using-latent-factors.html#one-hot-clustering"><i class="fa fa-check"></i><b>11.4.1</b> One-hot clustering</a></li>
<li class="chapter" data-level="11.4.2" data-path="clustering-using-latent-factors.html"><a href="clustering-using-latent-factors.html#k-means-clustering-1"><i class="fa fa-check"></i><b>11.4.2</b> K-means clustering</a></li>
</ul></li>
<li class="chapter" data-level="11.5" data-path="biological-interpretation-of-latent-factors.html"><a href="biological-interpretation-of-latent-factors.html"><i class="fa fa-check"></i><b>11.5</b> Biological interpretation of latent factors</a><ul>
<li class="chapter" data-level="11.5.1" data-path="biological-interpretation-of-latent-factors.html"><a href="biological-interpretation-of-latent-factors.html#inspection-of-feature-weights-in-loading-vectors"><i class="fa fa-check"></i><b>11.5.1</b> Inspection of feature weights in loading vectors</a></li>
<li class="chapter" data-level="11.5.2" data-path="biological-interpretation-of-latent-factors.html"><a href="biological-interpretation-of-latent-factors.html#making-sense-of-factors-using-enrichment-analysis"><i class="fa fa-check"></i><b>11.5.2</b> Making sense of factors using enrichment analysis</a></li>
<li class="chapter" data-level="11.5.3" data-path="biological-interpretation-of-latent-factors.html"><a href="biological-interpretation-of-latent-factors.html#interpretation-using-additional-covariates"><i class="fa fa-check"></i><b>11.5.3</b> Interpretation using additional covariates</a></li>
</ul></li>
<li class="chapter" data-level="11.6" data-path="exercises-9.html"><a href="exercises-9.html"><i class="fa fa-check"></i><b>11.6</b> Exercises</a><ul>
<li class="chapter" data-level="11.6.1" data-path="exercises-9.html"><a href="exercises-9.html#matrix-factorization-methods"><i class="fa fa-check"></i><b>11.6.1</b> Matrix factorization methods</a></li>
<li class="chapter" data-level="11.6.2" data-path="exercises-9.html"><a href="exercises-9.html#clustering-using-latent-factors-1"><i class="fa fa-check"></i><b>11.6.2</b> Clustering using latent factors</a></li>
<li class="chapter" data-level="11.6.3" data-path="exercises-9.html"><a href="exercises-9.html#biological-interpretation-of-latent-factors-1"><i class="fa fa-check"></i><b>11.6.3</b> Biological interpretation of latent factors</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i>References</a></li>
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<li><a href="https://bookdown.org" target="_blank">Published with bookdown</a></li>
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<h2><span class="header-section-number">7.6</span> Exercises</h2>
<p>For this set of exercises, we will use the <code>chip_1_1.fq.bz2</code> and <code>chip_2_1.fq.bz2</code> files from the <code>QuasR</code> package. You can reach the folder that contains the files as follows:</p>
<div class="sourceCode" id="cb382"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb382-1"><a href="exercises-5.html#cb382-1"></a>folder=(<span class="kw">system.file</span>(<span class="dt">package=</span><span class="st">"QuasR"</span>, <span class="st">"extdata"</span>))</span>
<span id="cb382-2"><a href="exercises-5.html#cb382-2"></a><span class="kw">dir</span>(folder) <span class="co"># will show the contents of the folder</span></span></code></pre></div>
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<li><p>Plot the base quality distributions of the ChIP-seq samples <code>Rqc</code> package.
<strong>HINT</strong>: You need to provide a regular expression pattern for extracting the right files from the folder. <code>"^chip"</code> matches the files beginning with “chip”. [Difficulty: <strong>Beginner/Intermediate</strong>]</p></li>
<li><p>Now we will trim the reads based on the quality scores. Let’s trim 2-4 bases on the 3’ end depending on the quality scores. You can use the <code>QuasR::preprocessReads()</code> function for this purpose. [Difficulty: <strong>Beginner/Intermediate</strong>]</p></li>
<li><p>Align the trimmed and untrimmed reads using <code>QuasR</code> and plot alignment statistics, did the trimming improve alignments? [Difficulty: <strong>Intermediate/Advanced</strong>]</p></li>
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