Skip to content

GitLab

Commit 8770eb71 authored by Christian Arnold's avatar Christian Arnold
Browse files

GRaNIE: Important bugfix for enrichment analyses: Introduced a regression in... 

GRaNIE: Important bugfix for enrichment analyses: Introduced a regression in 0.14 that is fixed now. Thanks to Nila for reporting it
parent 5695bbcf
Pipeline #28124 passed with stage
in 14 seconds
Expand all Hide whitespace changes
Inline Side-by-side
src/GRaNIE/DESCRIPTION
View file @ 8770eb71
Package: GRaNIE
Title: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data
Version: 0.14.2
Version: 0.14.3
Encoding: UTF-8
Authors@R: c(person("Christian", "Arnold", email =
"christian.arnold@embl.de", role = c("cre","aut")),
......
src/GRaNIE/R/core.R
View file @ 8770eb71
......@@ -4387,6 +4387,7 @@ calculateGeneralEnrichment <- function(GRN, ontology = c("BP", "MF"),
mapping = mapping)
GRN@stats[["Enrichment"]][["general"]] = general.enrichment
futile.logger::flog.info(paste0("Results stored in GRN@stats[[\"Enrichment\"]][[\"general\"]]"))
} else {
......@@ -4394,7 +4395,7 @@ calculateGeneralEnrichment <- function(GRN, ontology = c("BP", "MF"),
}
.printExecutionTime(start)
.printExecutionTime(start, prefix = "")
GRN
}
......@@ -4459,14 +4460,15 @@ calculateGeneralEnrichment <- function(GRN, ontology = c("BP", "MF"),
result.list = list()
# Construct a named vector with 0 or 1, 1 means in the foreground, 0 only in background
geneList = factor(as.integer(unique(background) %in% unique(foreground)))
names(geneList) = unique(background)
for (ontology_cur in ontology){
if (length(geneList == 0)) {
if (length(geneList) == 0) {
futile.logger::flog.warn(paste0("No enrichment found for ", ontology_cur, "."))
result.tbl = NULL
} else {
......@@ -4485,6 +4487,14 @@ calculateGeneralEnrichment <- function(GRN, ontology = c("BP", "MF"),
result.tbl = unique(topGO::GenTable(data, pval = result, orderBy = "pval", numChar = 1000,
topNodes = length(topGO::score(result))) )
result.tbl$GeneRatio = result.tbl$Significant / length(unique(foreground))
# Summmarize results
futile.logger::flog.info(paste0(" Enrichment calculation finished for ontology ", ontology_cur, ". Checked ", nrow(result.tbl), " terms"))
for (pvalueThres in c(0.01, 0.05, 0.1, 0.2)) {
dataCur = dplyr::filter(result.tbl, pval <= pvalueThres)
futile.logger::flog.info(paste0(" Number of terms for which p-value <= ", pvalueThres, ": ", nrow(dataCur)))
}
}
......@@ -4702,6 +4712,8 @@ calculateCommunitiesEnrichment <- function(GRN,
}
}
futile.logger::flog.info(paste0("Results stored in GRN@stats[[\"Enrichment\"]][[\"byCommunity\"]]"))
.printExecutionTime(start)
GRN
......
src/GRaNIE/docs/404.html
View file @ 8770eb71
......@@ -38,7 +38,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.2</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.3</span>
</span>
</div>
......
src/GRaNIE/docs/articles/Introduction.html
View file @ 8770eb71
This diff is collapsed.
src/GRaNIE/docs/articles/index.html
View file @ 8770eb71
......@@ -23,7 +23,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.2</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.3</span>
</span>
</div>
......
src/GRaNIE/docs/articles/quickStart.html
View file @ 8770eb71
......@@ -25,6 +25,8 @@
</script>
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-article">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
......@@ -37,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.14.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.3</span>
</span>
</div>
......@@ -84,13 +86,13 @@
</header><script src="quickStart_files/header-attrs-2.11/header-attrs.js"></script><div class="row">
</header><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Get Started with the <em>GRaNIE</em> packages from the Zaugg Lab</h1>
<h4 class="author">Christian Arnold, Judith Zaugg</h4>
<h4 data-toc-skip class="author">Christian Arnold, Judith Zaugg</h4>
<h4 class="date">14 December 2021</h4>
<h4 data-toc-skip class="date">15 December 2021</h4>
<div class="hidden name"><code>quickStart.Rmd</code></div>
......@@ -100,49 +102,46 @@
<p><strong>This vignette gives you a 1 minute summary of how to install and use our <em>GRaNIE</em> packages. For more details, check out the other Vignettes.</strong></p>
<div id="install-the-packages" class="section level2">
<h2 class="hasAnchor">
<a href="#install-the-packages" class="anchor"></a>Install the packages</h2>
<div id="stable-version-granie" class="section level3">
<h3 class="hasAnchor">
<a href="#stable-version-granie" class="anchor"></a>Stable version: <em>GRaNIE</em>
<div class="section level2">
<h2 id="install-the-packages">Install the packages<a class="anchor" aria-label="anchor" href="#install-the-packages"></a>
</h2>
<div class="section level3">
<h3 id="stable-version-granie">Stable version: <em>GRaNIE</em><a class="anchor" aria-label="anchor" href="#stable-version-granie"></a>
</h3>
<p>Installing our <em>GRaNIE</em> packages is easy. Just execute the following line into <em>R</em>:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://devtools.r-lib.org/">devtools</a></span><span class="op">)</span>
<span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html">install_gitlab</a></span><span class="op">(</span><span class="st">"grp-zaugg/GRaNIE"</span>, subdir <span class="op">=</span> <span class="st">"src/GRaNIE"</span>, host <span class="op">=</span> <span class="st">"git.embl.de"</span>, force <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://devtools.r-lib.org/" class="external-link">devtools</a></span><span class="op">)</span>
<span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html" class="external-link">install_gitlab</a></span><span class="op">(</span><span class="st">"grp-zaugg/GRaNIE"</span>, subdir <span class="op">=</span> <span class="st">"src/GRaNIE"</span>, host <span class="op">=</span> <span class="st">"git.embl.de"</span>, force <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
<p>If you receive an error message, make sure you installed the devtools package. If you don’t have it installed yet, just execute the following code into <em>R</em>:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"devtools"</span><span class="op">)</span></code></pre></div>
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"devtools"</span><span class="op">)</span></code></pre></div>
</div>
<div id="development-version-graniedev" class="section level3">
<h3 class="hasAnchor">
<a href="#development-version-graniedev" class="anchor"></a>Development version: <em>GRaNIEdev</em>
<div class="section level3">
<h3 id="development-version-graniedev">Development version: <em>GRaNIEdev</em><a class="anchor" aria-label="anchor" href="#development-version-graniedev"></a>
</h3>
<p>To install the development version of our <em>GRN</em> package, simply do:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html">install_gitlab</a></span><span class="op">(</span><span class="st">"grp-zaugg/GRaNIE"</span>, subdir <span class="op">=</span> <span class="st">"src/GRaNIEdev"</span>, host <span class="op">=</span> <span class="st">"git.embl.de"</span>, force <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html" class="external-link">install_gitlab</a></span><span class="op">(</span><span class="st">"grp-zaugg/GRaNIE"</span>, subdir <span class="op">=</span> <span class="st">"src/GRaNIEdev"</span>, host <span class="op">=</span> <span class="st">"git.embl.de"</span>, force <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
</div>
<div id="data-package-graniedata" class="section level3">
<h3 class="hasAnchor">
<a href="#data-package-graniedata" class="anchor"></a>Data package: <em>GRaNIEData</em>
<div class="section level3">
<h3 id="data-package-graniedata">Data package: <em>GRaNIEData</em><a class="anchor" aria-label="anchor" href="#data-package-graniedata"></a>
</h3>
<p>Similarly, to install the <em>GRaNIEData</em> package, simply do:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html">install_gitlab</a></span><span class="op">(</span><span class="st">"grp-zaugg/GRaNIE"</span>, subdir <span class="op">=</span> <span class="st">"src/GRaNIEData"</span>, host <span class="op">=</span> <span class="st">"git.embl.de"</span>, force <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html" class="external-link">install_gitlab</a></span><span class="op">(</span><span class="st">"grp-zaugg/GRaNIE"</span>, subdir <span class="op">=</span> <span class="st">"src/GRaNIEData"</span>, host <span class="op">=</span> <span class="st">"git.embl.de"</span>, force <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
</div>
</div>
<div id="what-do-the-different-packages-do" class="section level2">
<h2 class="hasAnchor">
<a href="#what-do-the-different-packages-do" class="anchor"></a>What do the different packages do?</h2>
<div class="section level2">
<h2 id="what-do-the-different-packages-do">What do the different packages do?<a class="anchor" aria-label="anchor" href="#what-do-the-different-packages-do"></a>
</h2>
<p>The stable version <strong><em>GRaNIE</em></strong> package is the best choice for most users, it contains features that have been tested more thoroughly and that we provide support for.</p>
<p>The development version <strong><em>GRaNIEdev</em></strong> contains new features that may or may not be tested so far and we can only provide limited support for it. This is the version we actively work on, and every once in a while after finishing a new feature, we integrate it into the stable version in the <em>GRaNIE</em> package.</p>
<p>The <strong><em>GRaNIEdata</em></strong> package provides example data that can be used to test the package and run the Vignettes.</p>
</div>
<div id="bug-reports-feature-requests-and-contact-information" class="section level2">
<h2 class="hasAnchor">
<a href="#bug-reports-feature-requests-and-contact-information" class="anchor"></a>Bug Reports, Feature Requests and Contact Information</h2>
<p>Please check out <strong><a href="https://grp-zaugg.embl-community.io/GRaNIE">https://grp-zaugg.embl-community.io/GRaNIE</a></strong> for how to get in contact with us.</p>
<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>
<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>
</div>
</div>
......@@ -157,11 +156,13 @@
<footer><div class="copyright">
<p>Developed by Christian Arnold, Rim Moussa.</p>
<p></p>
<p>Developed by Christian Arnold, Judith Zaugg, Rim Moussa.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
</div>
</footer>
......@@ -170,5 +171,7 @@
</body>
</html>
src/GRaNIE/docs/articles/workflow.html
View file @ 8770eb71
This diff is collapsed.
src/GRaNIE/docs/authors.html
View file @ 8770eb71
......@@ -23,7 +23,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.2</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.3</span>
</span>
</div>
......@@ -105,13 +105,13 @@
<p>Arnold C, Zaugg J, Moussa R (2021).
<em>GRaNIE: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data</em>.
R package version 0.14.2, <a href="https://grp-zaugg.embl-community.io/GRaNIE" class="external-link">https://grp-zaugg.embl-community.io/GRaNIE</a>.
R package version 0.14.3, <a href="https://grp-zaugg.embl-community.io/GRaNIE" class="external-link">https://grp-zaugg.embl-community.io/GRaNIE</a>.
</p>
<pre>@Manual{,
title = {GRaNIE: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data},
author = {Christian Arnold and Judith Zaugg and Rim Moussa},
year = {2021},
note = {R package version 0.14.2},
note = {R package version 0.14.3},
url = {https://grp-zaugg.embl-community.io/GRaNIE},
}</pre>
......
src/GRaNIE/docs/index.html
View file @ 8770eb71
......@@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.2</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.3</span>
</span>
</div>
......
src/GRaNIE/docs/news/index.html
View file @ 8770eb71
......@@ -23,7 +23,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.2</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.3</span>
</span>
</div>
......
src/GRaNIE/docs/pkgdown.yml
View file @ 8770eb71
......@@ -5,5 +5,5 @@ articles:
Introduction: Introduction.html
quickStart: quickStart.html
workflow: workflow.html
last_built: 2021-12-15T09:07Z
last_built: 2021-12-15T11:58Z
src/GRaNIE/docs/reference/AR_classification_wrapper.html
View file @ 8770eb71
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<head>
<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 the activator-repressor classification for the TFs for a GRN object — AR_classification_wrapper • GRaNIE</title>
<!-- 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 the activator-repressor classification for the TFs for a GRN object — AR_classification_wrapper" />
<meta property="og:description" content="Run the activator-repressor classification for the TFs for a GRN object" />
<!-- 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>Run the activator-repressor classification for the TFs for a GRN object — AR_classification_wrapper • GRaNIE</title><!-- 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 the activator-repressor classification for the TFs for a GRN object — AR_classification_wrapper"><meta property="og:description" content="Run the activator-repressor classification for the TFs for a GRN object"><!-- 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]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-530L9SXFM1"></script>
<script>
<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-530L9SXFM1"></script><script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-530L9SXFM1');
</script>
</head>
</script></head><body data-spy="scroll" data-target="#toc">
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
......@@ -82,13 +23,12 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.14.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.3</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<ul class="nav navbar-nav"><li>
<a href="../index.html"></a>
</li>
<li>
......@@ -100,8 +40,7 @@
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<ul class="dropdown-menu" role="menu"><li>
<a href="../articles/quickStart.html">Getting Started</a>
</li>
<li>
......@@ -110,119 +49,95 @@
<li>
<a href="../articles/workflow.html">Workflow example</a>
</li>
</ul>
</li>
</ul></li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
<a href="../news/index.html">Changelog &amp; News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
</header><div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Run the activator-repressor classification for the TFs for a <code><a href='GRN-class.html'>GRN</a></code> object</h1>
<h1>Run the activator-repressor classification for the TFs for a <code><a href="GRN-class.html">GRN</a></code> object</h1>
<div class="hidden name"><code>AR_classification_wrapper.Rd</code></div>
</div>
<div class="ref-description">
<p>Run the activator-repressor classification for the TFs for a <code><a href='GRN-class.html'>GRN</a></code> object</p>
<p>Run the activator-repressor classification for the TFs for a <code><a href="GRN-class.html">GRN</a></code> object</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">AR_classification_wrapper</span><span class="op">(</span>
<span class="va">GRN</span>,
significanceThreshold_Wilcoxon <span class="op">=</span> <span class="fl">0.05</span>,
plot_minNoTFBS_heatmap <span class="op">=</span> <span class="fl">100</span>,
deleteIntermediateData <span class="op">=</span> <span class="cn">TRUE</span>,
plotDiagnosticPlots <span class="op">=</span> <span class="cn">TRUE</span>,
outputFolder <span class="op">=</span> <span class="cn">NULL</span>,
corMethod <span class="op">=</span> <span class="st">"pearson"</span>,
forceRerun <span class="op">=</span> <span class="cn">FALSE</span>
<span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>GRN</dt>
<dd><p>Object of class <code><a href="GRN-class.html">GRN</a></code></p></dd>
<dt>significanceThreshold_Wilcoxon</dt>
<dd><p>Numeric between 0 and 1. Default 0.05. Significance threshold for Wilcoxon test that is run in the end for the final classification. See the Vignette and diffTF paper for details.</p></dd>
<dt>plot_minNoTFBS_heatmap</dt>
<dd><p>Integer. Default 100. Minimum number of TFBS for a TF to be included in the heatmap that is part of the output of this function.</p></dd>
<dt>deleteIntermediateData</dt>
<dd><p>TRUE or FALSE. Default <code>TRUE</code>. Should intermediate data be deleted before returning the object after a successful run? Due to the size of the produced intermediate data, we recommend setting this to <code>TRUE</code>, but if memory or object size are not an issue, the information can also be kept.</p></dd>
<dt>plotDiagnosticPlots</dt>
<dd><p>TRUE or FALSE. Default TRUE. Run and plot various diagnostic plots? If set to TRUE, PDF files will be produced and saved in the output directory (subfolder plots).</p></dd>
<dt>outputFolder</dt>
<dd><p>Character or NULL. Default NULL. If set to NULL, the default output folder as specified when initiating the object in <code>link{initializeGRN}</code> will be used. Otherwise, all output from this function will be put into the specified folder. We recommend specifiying an absolute path.</p></dd>
<dt>corMethod</dt>
<dd><p>Character. "pearson" or "spearman". Default "pearson". Method for calculating the correlation coefficient. See <a href="https://rdrr.io/r/stats/cor.html" class="external-link">cor</a> for details.</p></dd>
<dt>forceRerun</dt>
<dd><p>TRUE or FALSE. Default FALSE. Force execution, even if the GRN object already contains the result. Overwrites the old results.</p></dd>
</dl></div>
<div id="value">
<h2>Value</h2>
<p>The same <code><a href="GRN-class.html">GRN</a></code> object, with added data from this function. TF_classification_densityPlotsForegroundBackground_expression_perm0,1.pdf, TF_classification_stringencyThresholds_expression_perm0.pdf, TF_classification_summaryHeatmap_expression_perm0.pdf,</p>
</div>
<pre class="usage"><span class='fu'>AR_classification_wrapper</span><span class='op'>(</span>
<span class='va'>GRN</span>,
significanceThreshold_Wilcoxon <span class='op'>=</span> <span class='fl'>0.05</span>,
plot_minNoTFBS_heatmap <span class='op'>=</span> <span class='fl'>100</span>,
deleteIntermediateData <span class='op'>=</span> <span class='cn'>TRUE</span>,
plotDiagnosticPlots <span class='op'>=</span> <span class='cn'>TRUE</span>,
outputFolder <span class='op'>=</span> <span class='cn'>NULL</span>,
corMethod <span class='op'>=</span> <span class='st'>"pearson"</span>,
forceRerun <span class='op'>=</span> <span class='cn'>FALSE</span>
<span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>GRN</th>
<td><p>Object of class <code><a href='GRN-class.html'>GRN</a></code></p></td>
</tr>
<tr>
<th>significanceThreshold_Wilcoxon</th>
<td><p>Numeric between 0 and 1. Default 0.05. Significance threshold for Wilcoxon test that is run in the end for the final classification. See the Vignette and diffTF paper for details.</p></td>
</tr>
<tr>
<th>plot_minNoTFBS_heatmap</th>
<td><p>Integer. Default 100. Minimum number of TFBS for a TF to be included in the heatmap that is part of the output of this function.</p></td>
</tr>
<tr>
<th>deleteIntermediateData</th>
<td><p>TRUE or FALSE. Default <code>TRUE</code>. Should intermediate data be deleted before returning the object after a successful run? Due to the size of the produced intermediate data, we recommend setting this to <code>TRUE</code>, but if memory or object size are not an issue, the information can also be kept.</p></td>
</tr>
<tr>
<th>plotDiagnosticPlots</th>
<td><p>TRUE or FALSE. Default TRUE. Run and plot various diagnostic plots? If set to TRUE, PDF files will be produced and saved in the output directory (subfolder plots).</p></td>
</tr>
<tr>
<th>outputFolder</th>
<td><p>Character or NULL. Default NULL. If set to NULL, the default output folder as specified when initiating the object in <code>link{initializeGRN}</code> will be used. Otherwise, all output from this function will be put into the specified folder. We recommend specifiying an absolute path.</p></td>
</tr>
<tr>
<th>corMethod</th>
<td><p>Character. "pearson" or "spearman". Default "pearson". Method for calculating the correlation coefficient. See <a href='https://rdrr.io/r/stats/cor.html'>cor</a> for details.</p></td>
</tr>
<tr>
<th>forceRerun</th>
<td><p>TRUE or FALSE. Default FALSE. Force execution, even if the GRN object already contains the result. Overwrites the old results.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The same <code><a href='GRN-class.html'>GRN</a></code> object, with added data from this function. TF_classification_densityPlotsForegroundBackground_expression_perm0,1.pdf, TF_classification_stringencyThresholds_expression_perm0.pdf, TF_classification_summaryHeatmap_expression_perm0.pdf,</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='va'>GRN</span> <span class='op'>=</span> <span class='fu'>AR_classification_wrapper</span><span class='op'>(</span><span class='va'>GRN</span>, significanceThreshold_Wilcoxon <span class='op'>=</span> <span class='fl'>0.05</span>, plot_minNoTFBS_heatmap <span class='op'>=</span> <span class='fl'>100</span>, plotDiagnosticPlots <span class='op'>=</span> <span class='cn'>TRUE</span>, deleteIntermediateData <span class='op'>=</span> <span class='cn'>TRUE</span>, forceRerun <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='error'>Error in .addFunctionLogToObject(GRN): object 'GRN' not found</span></div></pre>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">GRN</span> <span class="op">=</span> <span class="fu">AR_classification_wrapper</span><span class="op">(</span><span class="va">GRN</span>, significanceThreshold_Wilcoxon <span class="op">=</span> <span class="fl">0.05</span>, plot_minNoTFBS_heatmap <span class="op">=</span> <span class="fl">100</span>, plotDiagnosticPlots <span class="op">=</span> <span class="cn">TRUE</span>, deleteIntermediateData <span class="op">=</span> <span class="cn">TRUE</span>, forceRerun <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .addFunctionLogToObject(GRN):</span> object 'GRN' not found</span>
</code></pre></div>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
<nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
</nav></div>
</div>
<footer>
<div class="copyright">
<p>Developed by Christian Arnold, Rim Moussa.</p>
<footer><div class="copyright">
<p></p><p>Developed by Christian Arnold, Judith Zaugg, Rim Moussa.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
</div>
</footer>
</div>
</footer></div>
</body>
</html>
</body></html>
src/GRaNIE/docs/reference/GRN-class.html
View file @ 8770eb71
......@@ -23,7 +23,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.2</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.3</span>
</span>
</div>
......
src/GRaNIE/docs/reference/GRaNIE.html
View file @ 8770eb71
......@@ -23,7 +23,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.3</span>
</span>
</div>
......@@ -102,7 +102,7 @@