Commit 357fb3fd authored by Christian Arnold's avatar Christian Arnold
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Documentation updates

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...@@ -5,7 +5,7 @@ This project is currently under active development. ...@@ -5,7 +5,7 @@ This project is currently under active development.
Repository structure Repository structure
---------------------- ----------------------
This repository for our `GRaNIE` packages (**G**ene **R**egul**a**tory **N**etwork **I**nference including **E**nhancers) currently contains everything that is related to this project and is organized into the following 3 packages: This repository for our *GRaNIE* packages (**G**ene **R**egul**a**tory **N**etwork **I**nference including **E**nhancers) currently contains everything that is related to this project and is organized into the following 3 packages:
- <code>GRaNIE</code> - <code>GRaNIE</code>
- <code>GRaNIEdata</code> (example dataset that the Vignette uses) - <code>GRaNIEdata</code> (example dataset that the Vignette uses)
...@@ -16,7 +16,7 @@ The full documentation for the all packages is available at the following stable ...@@ -16,7 +16,7 @@ The full documentation for the all packages is available at the following stable
**[https://grp-zaugg.embl-community.io/GRaNIE](https://grp-zaugg.embl-community.io/GRaNIE)** **[https://grp-zaugg.embl-community.io/GRaNIE](https://grp-zaugg.embl-community.io/GRaNIE)**
**We are soon submitting our `GRaNIE` and the associated `GRaNIEData` for being included on `Bioconductor`. Once we are accepted and the package is included in the stable release of `Bioconductor`, we will update the installation guidelines in the documentation.** **We are soon submitting our *GRaNIE* and the associated *GRaNIEData* for being included on *Bioconductor*. Once we are accepted and the package is included in the stable release of *Bioconductor*, we will update the installation guidelines in the documentation.**
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...@@ -19,7 +19,6 @@ ...@@ -19,7 +19,6 @@
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<script src="../pkgdown.js"></script><meta property="og:title" content="Package Details"> <script src="../pkgdown.js"></script><meta property="og:title" content="Package Details">
<meta property="og:description" content="GRaNIE"> <meta property="og:description" content="GRaNIE">
<meta property="og:image" content="/logo.png">
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...@@ -175,7 +174,7 @@ ...@@ -175,7 +174,7 @@
<h3 id="input_metadata">Sample metadata (optional but highly recommended)<a class="anchor" aria-label="anchor" href="#input_metadata"></a> <h3 id="input_metadata">Sample metadata (optional but highly recommended)<a class="anchor" aria-label="anchor" href="#input_metadata"></a>
</h3> </h3>
<p>Providing sample metadata is optional, but highly recommended - if available, the sample metadata is integrated into the PCA plots to understand where the variation in the data comes from and whether any of the metadata (e.g., age, sex, sequencing batch) is associated with the PCs from a PC, indicating a batch effect that needs to be addressed before running the <code>GRaNIE</code> pipeline.</p> <p>Providing sample metadata is optional, but highly recommended - if available, the sample metadata is integrated into the PCA plots to understand where the variation in the data comes from and whether any of the metadata (e.g., age, sex, sequencing batch) is associated with the PCs from a PC, indicating a batch effect that needs to be addressed before running the <code>GRaNIE</code> pipeline.</p>
<p>The integration of sample metadata can be achieved in the <code><a href="../reference/addData.html">addData()</a></code> function, see <code><a href="../reference/addData.html">?addData</a></code> for more information.</p> <p>The integration of sample metadata can be achieved in the <code><a href="../reference/addData.html">addData()</a></code> function (click the link for more information).</p>
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="input_HiC">Hi-C data (optional)<a class="anchor" aria-label="anchor" href="#input_HiC"></a> <h3 id="input_HiC">Hi-C data (optional)<a class="anchor" aria-label="anchor" href="#input_HiC"></a>
...@@ -319,7 +318,7 @@ ...@@ -319,7 +318,7 @@
<ol style="list-style-type: decimal"> <ol style="list-style-type: decimal">
<li>Multi-density plot across all samples (1 page)</li> <li>Multi-density plot across all samples (1 page)</li>
</ol> </ol>
<div class="figure"> <div class="figure" style="text-align: center">
<img src="figs/PCA_peaks_raw/p-01.png" alt="&lt;i&gt;Multi-density plot for read counts across all samples&lt;/i&gt;" width="80%"><p class="caption"> <img src="figs/PCA_peaks_raw/p-01.png" alt="&lt;i&gt;Multi-density plot for read counts across all samples&lt;/i&gt;" width="80%"><p class="caption">
<i>Multi-density plot for read counts across all samples</i> <i>Multi-density plot for read counts across all samples</i>
</p> </p>
...@@ -327,7 +326,7 @@ ...@@ -327,7 +326,7 @@
<ol start="2" style="list-style-type: decimal"> <ol start="2" style="list-style-type: decimal">
<li>Screeplot (1 page)</li> <li>Screeplot (1 page)</li>
</ol> </ol>
<div class="figure"> <div class="figure" style="text-align: center">
<img src="figs/PCA_peaks_raw/p-02.png" alt="&lt;i&gt;PCA screeplot&lt;/i&gt;" width="80%"><p class="caption"> <img src="figs/PCA_peaks_raw/p-02.png" alt="&lt;i&gt;PCA screeplot&lt;/i&gt;" width="80%"><p class="caption">
<i>PCA screeplot</i> <i>PCA screeplot</i>
</p> </p>
...@@ -335,7 +334,7 @@ ...@@ -335,7 +334,7 @@
<ol start="3" style="list-style-type: decimal"> <ol start="3" style="list-style-type: decimal">
<li>Metadata correlation plot</li> <li>Metadata correlation plot</li>
</ol> </ol>
<div class="figure"> <div class="figure" style="text-align: center">
<img src="figs/PCA_peaks_raw/p-03.png" alt="&lt;i&gt;Metadata correlation plot for PCA&lt;/i&gt;" width="80%"><p class="caption"> <img src="figs/PCA_peaks_raw/p-03.png" alt="&lt;i&gt;Metadata correlation plot for PCA&lt;/i&gt;" width="80%"><p class="caption">
<i>Metadata correlation plot for PCA</i> <i>Metadata correlation plot for PCA</i>
</p> </p>
...@@ -343,7 +342,7 @@ ...@@ -343,7 +342,7 @@
<ol start="4" style="list-style-type: decimal"> <ol start="4" style="list-style-type: decimal">
<li>PCA plots with different metadata being colored (5 or more pages, depending on available metadata)</li> <li>PCA plots with different metadata being colored (5 or more pages, depending on available metadata)</li>
</ol> </ol>
<div class="figure"> <div class="figure" style="text-align: center">
<img src="figs/PCA_peaks_raw/p-06.png" alt="&lt;i&gt;PCA plots for various metadata&lt;/i&gt;" width="100%"><p class="caption"> <img src="figs/PCA_peaks_raw/p-06.png" alt="&lt;i&gt;PCA plots for various metadata&lt;/i&gt;" width="100%"><p class="caption">
<i>PCA plots for various metadata</i> <i>PCA plots for various metadata</i>
</p> </p>
...@@ -354,7 +353,7 @@ ...@@ -354,7 +353,7 @@
<h3 id="output_TF_peak">TF-peak diagnostic plots<a class="anchor" aria-label="anchor" href="#output_TF_peak"></a> <h3 id="output_TF_peak">TF-peak diagnostic plots<a class="anchor" aria-label="anchor" href="#output_TF_peak"></a>
</h3> </h3>
<p>TF-peak diagnostic plots are available for each TF, and they currently look as follows:</p> <p>TF-peak diagnostic plots are available for each TF, and they currently look as follows:</p>
<div class="figure"> <div class="figure" style="text-align: center">
<img src="figs/TFPeak_fdr_orig/p-25.png" alt="&lt;i&gt;TF-peak diagnostic plots for an example TF&lt;/i&gt;" width="100%"><p class="caption"> <img src="figs/TFPeak_fdr_orig/p-25.png" alt="&lt;i&gt;TF-peak diagnostic plots for an example TF&lt;/i&gt;" width="100%"><p class="caption">
<i>TF-peak diagnostic plots for an example TF</i> <i>TF-peak diagnostic plots for an example TF</i>
</p> </p>
...@@ -372,7 +371,7 @@ ...@@ -372,7 +371,7 @@
<strong>Summary heatmaps (files starting with <code>TF_classification_summaryHeatmap</code>)</strong>: <a href="https://difftf.readthedocs.io/en/latest/chapter2.html#files-comparisontype-diagnosticplotsclassification1-pdf-and-comparisontype-diagnosticplotsclassification2-pdf" class="external-link">This is described in detail in the <code>diffTF</code> documentation.</a> <strong>Summary heatmaps (files starting with <code>TF_classification_summaryHeatmap</code>)</strong>: <a href="https://difftf.readthedocs.io/en/latest/chapter2.html#files-comparisontype-diagnosticplotsclassification1-pdf-and-comparisontype-diagnosticplotsclassification2-pdf" class="external-link">This is described in detail in the <code>diffTF</code> documentation.</a>
</li> </li>
</ol> </ol>
<div class="figure"> <div class="figure" style="text-align: center">
<img src="figs/AR_heatmap_expr_real/p-1.png" alt="&lt;i&gt;AR summary heatmap&lt;/i&gt;" width="60%"><p class="caption"> <img src="figs/AR_heatmap_expr_real/p-1.png" alt="&lt;i&gt;AR summary heatmap&lt;/i&gt;" width="60%"><p class="caption">
<i>AR summary heatmap</i> <i>AR summary heatmap</i>
</p> </p>
...@@ -382,8 +381,8 @@ ...@@ -382,8 +381,8 @@
<strong>Summary stringency plots (files starting with <code>TF_classification_stringencyThresholds</code>)</strong>: <a href="https://difftf.readthedocs.io/en/latest/chapter2.html#files-comparisontype-diagnosticplotsclassification1-pdf-and-comparisontype-diagnosticplotsclassification2-pdf" class="external-link">This is described in detail in the <code>diffTF</code> documentation.</a> <strong>Summary stringency plots (files starting with <code>TF_classification_stringencyThresholds</code>)</strong>: <a href="https://difftf.readthedocs.io/en/latest/chapter2.html#files-comparisontype-diagnosticplotsclassification1-pdf-and-comparisontype-diagnosticplotsclassification2-pdf" class="external-link">This is described in detail in the <code>diffTF</code> documentation.</a>
</li> </li>
</ol> </ol>
<div class="figure"> <div class="figure" style="text-align: center">
<img src="figs/AR_stringency_expr_real/p-1.png" alt="&lt;i&gt;AR stringency thresholds&lt;/i&gt;" width="60%"><p class="caption"> <img src="figs/AR_stringency_expr_real/p-1.png" alt="&lt;i&gt;AR stringency thresholds&lt;/i&gt;" width="40%"><p class="caption">
<i>AR stringency thresholds</i> <i>AR stringency thresholds</i>
</p> </p>
</div> </div>
...@@ -391,7 +390,7 @@ ...@@ -391,7 +390,7 @@
<li> <li>
<strong>Density plots per TF (files starting with <code>TF_classification_densityPlotsForegroundBackground</code>)</strong>: Density plots for each TF, with one TF per page. The plot shows the foreground (red, labeled as <code>Motif</code>) and background (gray, labeled as <code>Non-motif</code>) densities of the correlation coefficient (either Pearson or Spearman, see x-axis label) from peaks with (foreground) or without (background) a (predicted) TFBS in the peak for the particular TF. The numbers in the parenthesis summarize the underlying total number of peaks.</li> <strong>Density plots per TF (files starting with <code>TF_classification_densityPlotsForegroundBackground</code>)</strong>: Density plots for each TF, with one TF per page. The plot shows the foreground (red, labeled as <code>Motif</code>) and background (gray, labeled as <code>Non-motif</code>) densities of the correlation coefficient (either Pearson or Spearman, see x-axis label) from peaks with (foreground) or without (background) a (predicted) TFBS in the peak for the particular TF. The numbers in the parenthesis summarize the underlying total number of peaks.</li>
</ol> </ol>
<div class="figure"> <div class="figure" style="text-align: center">
<img src="figs/AR_density_expr_real/p-06.png" alt="&lt;i&gt;Density plots per TF&lt;/i&gt;" width="60%"><p class="caption"> <img src="figs/AR_density_expr_real/p-06.png" alt="&lt;i&gt;Density plots per TF&lt;/i&gt;" width="60%"><p class="caption">
<i>Density plots per TF</i> <i>Density plots per TF</i>
</p> </p>
...@@ -403,7 +402,7 @@ ...@@ -403,7 +402,7 @@
</h3> </h3>
<p>We provide a number of diagnostic plots for the peak-gene links that are imperative for understanding the biological system and GRN. In what follows, we describe them briefly, along with some notes on expected patterns, implications etc. Note that this section is subject to continuous change.</p> <p>We provide a number of diagnostic plots for the peak-gene links that are imperative for understanding the biological system and GRN. In what follows, we describe them briefly, along with some notes on expected patterns, implications etc. Note that this section is subject to continuous change.</p>
<p>We currently offer a summary QC figure for the peak-gene connections that looks as follows:</p> <p>We currently offer a summary QC figure for the peak-gene connections that looks as follows:</p>
<div class="figure"> <div class="figure" style="text-align: center">
<img src="figs/peakGene_QC_all/p-1.png" alt="&lt;i&gt;Summary peak-gene QC figure&lt;/i&gt;" width="100%"><p class="caption"> <img src="figs/peakGene_QC_all/p-1.png" alt="&lt;i&gt;Summary peak-gene QC figure&lt;/i&gt;" width="100%"><p class="caption">
<i>Summary peak-gene QC figure</i> <i>Summary peak-gene QC figure</i>
</p> </p>
...@@ -431,14 +430,14 @@ ...@@ -431,14 +430,14 @@
<p>For the <code>r+</code> / <code>r-</code> dimension and permuted data, the ratios should be close to 1 across all p-value bins, while for the real data, a high ratio is typically seen for small p-values. In general, the difference between the permuted and real bar should be large for small p-values and close to 1 for larger ones.</p> <p>For the <code>r+</code> / <code>r-</code> dimension and permuted data, the ratios should be close to 1 across all p-value bins, while for the real data, a high ratio is typically seen for small p-values. In general, the difference between the permuted and real bar should be large for small p-values and close to 1 for larger ones.</p>
<p>For the real / permuted dimension, what we want to see is again a high ratio for small p-value bins for the <code>r+</code> links, indicating that when comparing permuted vs real, there are many more small p-value links in real data as compared to permuted. This usually does not hold true for the <code>r-</code> links, though, as can be seen also from the plot: the gray bars are smaller and closer to 1 across the whole binned p-value range.</p> <p>For the real / permuted dimension, what we want to see is again a high ratio for small p-value bins for the <code>r+</code> links, indicating that when comparing permuted vs real, there are many more small p-value links in real data as compared to permuted. This usually does not hold true for the <code>r-</code> links, though, as can be seen also from the plot: the gray bars are smaller and closer to 1 across the whole binned p-value range.</p>
<p>Lastly, we can also stratify the raw p-value distribution for <code>r+</code> and <code>r-</code> peak-gene connections according to different biological properties such as the peak-gene distance and others (see below). Here, we focus solely on the real data and additionally stratify the p-value distributions of peak-gene links by their genomic distance (measured as the distance of the middle of the peak to the TSS of the gene, in base pairs). For this, we bin the peak-gene distance equally into 10 bins, which results in the bins containing a non-equal number of data points but genomic distance is increased uniformly from bin to bin:</p> <p>Lastly, we can also stratify the raw p-value distribution for <code>r+</code> and <code>r-</code> peak-gene connections according to different biological properties such as the peak-gene distance and others (see below). Here, we focus solely on the real data and additionally stratify the p-value distributions of peak-gene links by their genomic distance (measured as the distance of the middle of the peak to the TSS of the gene, in base pairs). For this, we bin the peak-gene distance equally into 10 bins, which results in the bins containing a non-equal number of data points but genomic distance is increased uniformly from bin to bin:</p>
<div class="figure"> <div class="figure" style="text-align: center">
<img src="figs/peakGene_QC_all/p-2.png" alt="&lt;i&gt;Density of raw p-values, stratified by (1) peak-gene distance (using equally sized bins) and (2) `r+` / `r-` links&lt;/i&gt;" width="80%"><p class="caption"> <img src="figs/peakGene_QC_all/p-2.png" alt="&lt;i&gt;Density of raw p-values, stratified by (1) peak-gene distance (using equally sized bins) and (2) `r+` / `r-` links&lt;/i&gt;" width="80%"><p class="caption">
<i>Density of raw p-values, stratified by (1) peak-gene distance (using equally sized bins) and (2) <code>r+</code> / <code>r-</code> links</i> <i>Density of raw p-values, stratified by (1) peak-gene distance (using equally sized bins) and (2) <code>r+</code> / <code>r-</code> links</i>
</p> </p>
</div> </div>
<p>We generally (hope to) see that for smaller peak-gene distances (in particular those that overlap, i.e., the peak and the gene are in direct vicinity or even overlapping), the difference between r+ and r- links is bigger as for more distant links. We also include the random links, for which no difference between r+ and r- links is visible, as expected for a well-calibrated background.</p> <p>We generally (hope to) see that for smaller peak-gene distances (in particular those that overlap, i.e., the peak and the gene are in direct vicinity or even overlapping), the difference between r+ and r- links is bigger as for more distant links. We also include the random links, for which no difference between r+ and r- links is visible, as expected for a well-calibrated background.</p>
<p>Let’s plot the same, but stratified by peak-gene distance and <code>r+</code> / <code>r-</code> within each plot instead:</p> <p>Let’s plot the same, but stratified by peak-gene distance and <code>r+</code> / <code>r-</code> within each plot instead:</p>
<div class="figure"> <div class="figure" style="text-align: center">
<img src="figs/peakGene_QC_all/p-3.png" alt="&lt;i&gt;Density of raw p-values, stratified by (1) peak-gene distance (using equally sized bins) and (2) `r+` / `r-` links&lt;/i&gt;" width="80%"><p class="caption"> <img src="figs/peakGene_QC_all/p-3.png" alt="&lt;i&gt;Density of raw p-values, stratified by (1) peak-gene distance (using equally sized bins) and (2) `r+` / `r-` links&lt;/i&gt;" width="80%"><p class="caption">
<i>Density of raw p-values, stratified by (1) peak-gene distance (using equally sized bins) and (2) <code>r+</code> / <code>r-</code> links</i> <i>Density of raw p-values, stratified by (1) peak-gene distance (using equally sized bins) and (2) <code>r+</code> / <code>r-</code> links</i>
</p> </p>
...@@ -448,7 +447,7 @@ ...@@ -448,7 +447,7 @@
<h4 id="correlation-coefficient-distribution">Correlation coefficient distribution<a class="anchor" aria-label="anchor" href="#correlation-coefficient-distribution"></a> <h4 id="correlation-coefficient-distribution">Correlation coefficient distribution<a class="anchor" aria-label="anchor" href="#correlation-coefficient-distribution"></a>
</h4> </h4>
<p>So far, we analyzed the raw p-value distribution in detail. Let’s focus now on the distribution of the correlation coefficient per se.</p> <p>So far, we analyzed the raw p-value distribution in detail. Let’s focus now on the distribution of the correlation coefficient per se.</p>
<div class="figure"> <div class="figure" style="text-align: center">
<img src="figs/peakGene_QC_all/p-4.png" alt="&lt;i&gt;Density of the correlation coefficient, stratified by (1) peak-gene distance (using equally sized bins)&lt;/i&gt;" width="80%"><p class="caption"> <img src="figs/peakGene_QC_all/p-4.png" alt="&lt;i&gt;Density of the correlation coefficient, stratified by (1) peak-gene distance (using equally sized bins)&lt;/i&gt;" width="80%"><p class="caption">
<i>Density of the correlation coefficient, stratified by (1) peak-gene distance (using equally sized bins)</i> <i>Density of the correlation coefficient, stratified by (1) peak-gene distance (using equally sized bins)</i>
</p> </p>
...@@ -470,14 +469,14 @@ ...@@ -470,14 +469,14 @@
</ol> </ol>
<p>Both plot types compare the connectivity for the real and permuted data (denoted as <code>Network type</code> in the boxplot PDF), which allows a better judgment of the connectivity from the real data.</p> <p>Both plot types compare the connectivity for the real and permuted data (denoted as <code>Network type</code> in the boxplot PDF), which allows a better judgment of the connectivity from the real data.</p>
<p>An example page for the summary heatmap looks like this:</p> <p>An example page for the summary heatmap looks like this:</p>
<div class="figure"> <div class="figure" style="text-align: center">
<img src="figs/connectionsHeatmap/p-3.png" alt="&lt;i&gt;Example heatmap for the connection summary&lt;/i&gt;" width="80%"><p class="caption"> <img src="figs/connectionsHeatmap/p-3.png" alt="&lt;i&gt;Example heatmap for the connection summary&lt;/i&gt;" width="80%"><p class="caption">
<i>Example heatmap for the connection summary</i> <i>Example heatmap for the connection summary</i>
</p> </p>
</div> </div>
<p>Here, two heatmaps are shown, one for real (top) and one for permuted (bottom) network. Each of them shows for different combinations of TF-peak and peak-gene FDRs (0.01 to 0.2) the number of unique node types for the given FDR combination (here: TFs).</p> <p>Here, two heatmaps are shown, one for real (top) and one for permuted (bottom) network. Each of them shows for different combinations of TF-peak and peak-gene FDRs (0.01 to 0.2) the number of unique node types for the given FDR combination (here: TFs).</p>
<p>Second, a multi-page summary PDF for the connections in form of a boxplot, as exemplified with the following Figure:</p> <p>Second, a multi-page summary PDF for the connections in form of a boxplot, as exemplified with the following Figure:</p>
<div class="figure"> <div class="figure" style="text-align: center">
<img src="figs/connectionsBoxplot/p-04.png" alt="&lt;i&gt;Example boxplot for the connection summary&lt;/i&gt;" width="80%"><p class="caption"> <img src="figs/connectionsBoxplot/p-04.png" alt="&lt;i&gt;Example boxplot for the connection summary&lt;/i&gt;" width="80%"><p class="caption">
<i>Example boxplot for the connection summary</i> <i>Example boxplot for the connection summary</i>
</p> </p>
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<script src="../pkgdown.js"></script><meta property="og:title" content="Get Started with the *GRaNIE* packages from the Zaugg Lab"> <script src="../pkgdown.js"></script><meta property="og:title" content="Get Started with the *GRaNIE* packages from the Zaugg Lab">
<meta property="og:description" content="GRaNIE"> <meta property="og:description" content="GRaNIE">
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<div class="section level2"> <div class="section level2">
<h2 id="bug-reports-feature-requests-and-contact-information">Bug Reports, Feature Requests and Contact Information<a class="anchor" aria-label="anchor" href="#bug-reports-feature-requests-and-contact-information"></a> <h2 id="bug-reports-feature-requests-and-contact-information">Bug Reports, Feature Requests and Contact Information<a class="anchor" aria-label="anchor" href="#bug-reports-feature-requests-and-contact-information"></a>
</h2> </h2>
<p>Please check out <strong><a href="https://grp-zaugg.embl-community.io/GRaNIE" class="external-link">https://grp-zaugg.embl-community.io/GRaNIE</a></strong> for how to get in contact with us.</p> <p>Please check out <strong><a href="https://grp-zaugg.embl-community.io/GRaNIE" class="external-link">the main page</a></strong> for how to get in contact with us.</p>
</div> </div>
</div> </div>
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...@@ -5,5 +5,5 @@ articles: ...@@ -5,5 +5,5 @@ articles:
packageDetails: packageDetails.html packageDetails: packageDetails.html
quickStart: quickStart.html quickStart: quickStart.html
workflow: workflow.html workflow: workflow.html
last_built: 2022-01-21T11:22Z last_built: 2022-01-21T12:15Z
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>GRaNIE (Gene Regulatory Network Inference including Enhancers): Reconstruction and evaluation of data-driven, cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNAseq data (general package information) — GRaNIE • GRaNIE</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="GRaNIE (Gene Regulatory Network Inference including Enhancers): Reconstruction and evaluation of data-driven, cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNAseq data (general package information) — GRaNIE"><meta property="og:description" content="Genetic variants associated with diseases often affect non-coding regions, thus likely having a regulatory role. To understand the effects of genetic variants in these regulatory regions, identifying genes that are modulated by specific regulatory elements (REs) is crucial. The effect of gene regulatory elements, such as enhancers, is often cell-type specific, likely because the combinations of transcription factors (TFs) that are regulating a given enhancer have celltype specific activity. This TF activity can be quantified with existing tools such as diffTF and captures differences in binding of a TF in open chromatin regions. Collectively, this forms a gene regulatory network (eGRN) with cell-type and data-specific TF-RE and RE-gene links. Here, we reconstruct such a eGRN using bulk RNAseq and open chromatin (e.g., using ATACseq or ChIPseq for open chromatin marks) and optionally TF activity data. Our network contains different types of links, connecting TFs to regulatory elements, the latter of which is connected to genes in the vicinity or within the same chromatin domain (TAD). We use a statistical framework to assign empirical FDRs and weights to all links using a permutation-based approach."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>GRaNIE (Gene Regulatory Network Inference including Enhancers): Reconstruction and evaluation of data-driven, cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNAseq data (general package information) — GRaNIE • GRaNIE</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="GRaNIE (Gene Regulatory Network Inference including Enhancers): Reconstruction and evaluation of data-driven, cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNAseq data (general package information) — GRaNIE"><meta property="og:description" content="Genetic variants associated with diseases often affect non-coding regions, thus likely having a regulatory role. To understand the effects of genetic variants in these regulatory regions, identifying genes that are modulated by specific regulatory elements (REs) is crucial. The effect of gene regulatory elements, such as enhancers, is often cell-type specific, likely because the combinations of transcription factors (TFs) that are regulating a given enhancer have celltype specific activity. This TF activity can be quantified with existing tools such as diffTF and captures differences in binding of a TF in open chromatin regions. Collectively, this forms a gene regulatory network (eGRN) with cell-type and data-specific TF-RE and RE-gene links. Here, we reconstruct such a eGRN using bulk RNAseq and open chromatin (e.g., using ATACseq or ChIPseq for open chromatin marks) and optionally TF activity data. Our network contains different types of links, connecting TFs to regulatory elements, the latter of which is connected to genes in the vicinity or within the same chromatin domain (TAD). We use a statistical framework to assign empirical FDRs and weights to all links using a permutation-based approach."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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Note that raw p-values are not adjusted. — add_TF_gene_correlation • GRaNIE</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Add TF-gene correlations to a GRN object. The information is currently stored in GRN@connections$TF_genes.filtered. Note that raw p-values are not adjusted. — add_TF_gene_correlation"><meta property="og:description" content="Add TF-gene correlations to a GRN object. The information is currently stored in GRN@connections$TF_genes.filtered. Note that raw p-values are not adjusted."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Add TF-gene correlations to a GRN object. The information is currently stored in GRN@connections$TF_genes.filtered. Note that raw p-values are not adjusted. — add_TF_gene_correlation • GRaNIE</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Add TF-gene correlations to a GRN object. The information is currently stored in GRN@connections$TF_genes.filtered. Note that raw p-values are not adjusted. — add_TF_gene_correlation"><meta property="og:description" content="Add TF-gene correlations to a GRN object. The information is currently stored in GRN@connections$TF_genes.filtered. Note that raw p-values are not adjusted."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Enrichment analysis for the genes in each community in the filtered GRN — calculateCommunitiesEnrichment • GRaNIE</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Enrichment analysis for the genes in each community in the filtered GRN — calculateCommunitiesEnrichment"><meta property="og:description" content="After the vertices of the filtered GRN are clustered into communities using calculateCommunitiesStats, this function will run a per-community enrichment analysis."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Enrichment analysis for the genes in each community in the filtered GRN — calculateCommunitiesEnrichment • GRaNIE</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Enrichment analysis for the genes in each community in the filtered GRN — calculateCommunitiesEnrichment"><meta property="og:description" content="After the vertices of the filtered GRN are clustered into communities using calculateCommunitiesStats, this function will run a per-community enrichment analysis."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Run an enrichment analysis for the genes in the filtered GRN — calculateGeneralEnrichment • GRaNIE</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Run an enrichment analysis for the genes in the filtered GRN — calculateGeneralEnrichment"><meta property="og:description" content="This function runs an enrichment analysis for the genes in the filtered network."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Calculate TF-based GO enrichment — calculateTFEnrichment • GRaNIE</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate TF-based GO enrichment — calculateTFEnrichment"><meta property="og:description" content="This function calculates the GO enrichment per TF, i.e. for the set of genes a given TF is connected to in the filtered GRN."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Calculate TF-based GO enrichment — calculateTFEnrichment • GRaNIE</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate TF-based GO enrichment — calculateTFEnrichment"><meta property="og:description" content="This function calculates the GO enrichment per TF, i.e. for the set of genes a given TF is connected to in the filtered GRN."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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