P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2024-12-26 20:46:12 +01:00
Code Releases Activity
94ecdb9614
AMR/reference/export_ncbi_biosample.html

102 lines
9.7 KiB
HTML
Raw Normal View History

cli-147-2111
2024-06-10 10:40:19 +02:00
<!DOCTYPE html>
Built site for AMR@2.1.1.9103: 87271d2
2024-11-21 10:17:08 +01:00
<!-- 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, shrink-to-fit=no"><title>Export Data Set as NCBI BioSample Antibiogram — export_ncbi_biosample • AMR (for R)</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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Export Data Set as NCBI BioSample Antibiogram — export_ncbi_biosample"><meta name="description" content="Export Data Set as NCBI BioSample Antibiogram"><meta property="og:description" content="Export Data Set as NCBI BioSample Antibiogram"><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"></head><body>
cli-147-2111
2024-06-10 10:40:19 +02:00
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
Built site for AMR@2.1.1.9063: 640888f
2024-07-16 15:00:55 +02:00
<nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
cli-147-2111
2024-06-10 10:40:19 +02:00
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
Built site for AMR@2.1.1.9109: 7f4ea96
2024-11-21 22:10:41 +01:00
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9109</small>
Built site for AMR@2.1.1.9063: 640888f
2024-07-16 15:00:55 +02:00
cli-147-2111
2024-06-10 10:40:19 +02:00
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div id="navbar" class="collapse navbar-collapse ms-3">
<ul class="navbar-nav me-auto"><li class="nav-item dropdown">
Built site for AMR@2.1.1.9063: 640888f
2024-07-16 15:00:55 +02:00
<button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
<ul class="dropdown-menu" aria-labelledby="dropdown-how-to"><li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
<li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
<li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
</ul></li>
Built site for AMR@2.1.1.9084: 9141546
2024-09-30 22:12:21 +02:00
<li class="nav-item"><a class="nav-link" href="../articles/AMR_for_Python.html"><span class="fa fab fa-python"></span> AMR for Python</a></li>
Built site for AMR@2.1.1.9063: 640888f
2024-07-16 15:00:55 +02:00
<li class="active nav-item"><a class="nav-link" href="../reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
<li class="nav-item"><a class="nav-link" href="../authors.html"><span class="fa fa-users"></span> Authors</a></li>
</ul><ul class="navbar-nav"><li class="nav-item"><a class="nav-link" href="../news/index.html"><span class="fa far fa-newspaper"></span> Changelog</a></li>
<li class="nav-item"><a class="external-link nav-link" href="https://github.com/msberends/AMR"><span class="fa fab fa-github"></span> Source Code</a></li>
cli-147-2111
2024-06-10 10:40:19 +02:00
</ul></div>
Built site for AMR@2.1.1.9063: 640888f
2024-07-16 15:00:55 +02:00
cli-147-2111
2024-06-10 10:40:19 +02:00
</div>
</nav><div class="container template-reference-topic">
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Export Data Set as NCBI BioSample Antibiogram</h1>
Built site for AMR@2.1.1.9063: 640888f
2024-07-16 15:00:55 +02:00
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/export_biosample.R" class="external-link"><code>R/export_biosample.R</code></a></small>
cli-147-2111
2024-06-10 10:40:19 +02:00
<div class="d-none name"><code>export_ncbi_biosample.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Export Data Set as NCBI BioSample Antibiogram</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">export_ncbi_biosample</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> filename <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"biosample_"</span>, <span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">"%Y-%m-%d-%H%M%S"</span><span class="op">)</span>, <span class="st">".xlsx"</span><span class="op">)</span>,</span>
<span> type <span class="op">=</span> <span class="st">"pathogen MIC"</span>,</span>
<span> columns <span class="op">=</span> <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>,</span>
<span> save_as_xlsx <span class="op">=</span> <span class="cn">TRUE</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
Built site for AMR@2.1.1.9063: 640888f
2024-07-16 15:00:55 +02:00
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
cli-147-2111
2024-06-10 10:40:19 +02:00
<dd><p>a data set</p></dd>
Built site for AMR@2.1.1.9063: 640888f
2024-07-16 15:00:55 +02:00
<dt id="arg-filename">filename<a class="anchor" aria-label="anchor" href="#arg-filename"></a></dt>
cli-147-2111
2024-06-10 10:40:19 +02:00
<dd><p>a character string specifying the file name</p></dd>
Built site for AMR@2.1.1.9063: 640888f
2024-07-16 15:00:55 +02:00
<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt>
cli-147-2111
2024-06-10 10:40:19 +02:00
<dd><p>a character string specifying the type of data set, either "pathogen MIC" or "beta-lactamase MIC", see <a href="https://www.ncbi.nlm.nih.gov/biosample/docs/" class="external-link">https://www.ncbi.nlm.nih.gov/biosample/docs/</a></p></dd>
</dl></div>
Built site for AMR@2.1.1.9063: 640888f
2024-07-16 15:00:55 +02:00
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
cli-147-2111
2024-06-10 10:40:19 +02:00
</nav></aside></div>
<footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
</div>
<div class="pkgdown-footer-right">
Built site for AMR@2.1.1.9077: 28bf91c
2024-09-19 14:48:19 +02:00
<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style="max-width: 150px;"></a></p>
cli-147-2111
2024-06-10 10:40:19 +02:00
</div>
</footer></div>
Built site for AMR@2.1.1.9063: 640888f
2024-07-16 15:00:55 +02:00
cli-147-2111
2024-06-10 10:40:19 +02:00
</body></html>
Copy Permalink