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<h1 class="title">HPC_tidymass流程开发</h1>
</div>
<div class="quarto-title-meta">
<div>
<div class="quarto-title-meta-heading">Author</div>
<div class="quarto-title-meta-contents">
<p>Shawn </p>
</div>
</div>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">February 11, 2023</p>
</div>
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<center>
<p><font color="salmon" size="2pt"> 🏡Zhang Lab, February, 2023 🏡</font></p>
<p><font color="green" size="2pt"> 🔬Multi-omics research center, HENU, Kaifeng, Henan 🔬</font></p>
<p><font color="green" size="2pt"> 🔬State Key Laboratory of Crop Stress Adaption and Improvement, HENU, Kaifeng, Henan 🔬</font></p>
</center>
<section id="需要搭建的环境" class="level1">
<h1>需要搭建的环境：</h1>
<p>首先联系管理员开通linux账户。然后并将账户添加到<code>bio</code>和<code>docker</code>用户组。<code>bio</code>账户是我们上传原始数据的账户，在数据格式转换的时候需要用到<code>docker</code>,在linux系统下，只有<code>root</code>账号可以使用<code>docker</code>，这时我们需要创建一个<code>docker</code>的用户组，将需要使用<code>tidymass</code>流程账号纳入<code>docker group</code>。<br>
检查是否属于<code>docker</code> 用户组可以通过在终端输入<code>groups</code>进行组别查看：</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>shawn<span class="sc">@</span>bio<span class="sc">-</span>Super<span class="sc">-</span>Server<span class="sc">:</span><span class="er">~$</span> groups</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>root sudo docker bio teacher</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>其次需要安装<code>tidyvers</code>,<code>tidymass</code>以及我写的<code>MDAtoolkits</code>和<code>IMOtoolkits</code>包。同样通过下列代码查看依赖包是否安装好。</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>shawn<span class="sc">@</span>bio<span class="sc">-</span>Super<span class="sc">-</span>Server<span class="sc">:</span><span class="er">~$</span> R <span class="do">## 终端输入R回车</span></span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>R version <span class="dv">4</span>.<span class="fl">1.2</span> (<span class="dv">2021-11-01</span>) <span class="sc">--</span> <span class="st">"Bird Hippie"</span></span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="fu">Copyright</span> (C) <span class="dv">2021</span> The R Foundation <span class="cf">for</span> Statistical Computing</span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>Platform<span class="sc">:</span> x86_64<span class="sc">-</span>pc<span class="sc">-</span>linux<span class="sc">-</span><span class="fu">gnu</span> (<span class="dv">64</span><span class="sc">-</span>bit)</span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a>R is free software and comes with ABSOLUTELY NO WARRANTY.</span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a>You are welcome to redistribute it under certain conditions.</span>
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a>Type <span class="st">'license()'</span> or <span class="st">'licence()'</span> <span class="cf">for</span> distribution details.</span>
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a>R is a collaborative project with many contributors.</span>
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a>Type <span class="st">'contributors()'</span> <span class="cf">for</span> more information and</span>
<span id="cb2-13"><a href="#cb2-13" aria-hidden="true" tabindex="-1"></a><span class="st">'citation()'</span> on how to cite R or R packages <span class="cf">in</span> publications.</span>
<span id="cb2-14"><a href="#cb2-14" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-15"><a href="#cb2-15" aria-hidden="true" tabindex="-1"></a>Type <span class="st">'demo()'</span> <span class="cf">for</span> some demos, <span class="st">'help()'</span> <span class="cf">for</span> on<span class="sc">-</span>line help, or</span>
<span id="cb2-16"><a href="#cb2-16" aria-hidden="true" tabindex="-1"></a><span class="st">'help.start()'</span> <span class="cf">for</span> an HTML browser interface to help.</span>
<span id="cb2-17"><a href="#cb2-17" aria-hidden="true" tabindex="-1"></a>Type <span class="st">'q()'</span> to quit R.</span>
<span id="cb2-18"><a href="#cb2-18" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-19"><a href="#cb2-19" aria-hidden="true" tabindex="-1"></a><span class="do">##> 加载包，没有ERROR报错说明装好了。</span></span>
<span id="cb2-20"><a href="#cb2-20" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidymass)</span>
<span id="cb2-21"><a href="#cb2-21" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyverse)</span>
<span id="cb2-22"><a href="#cb2-22" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(MDAtoolkits)</span>
<span id="cb2-23"><a href="#cb2-23" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(IMOtoolkits)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>环境初始化: 首先通过下列命令创建脚本存放路径</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>cd <span class="do">## 回到家目录</span></span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="do">##> 第一步 创建脚本存放路径</span></span>
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a>mkdir <span class="sc">-</span>p <span class="sc">/</span><span class="fl">01.</span>src<span class="sc">/</span><span class="fl">02.</span>script<span class="sc">/</span><span class="fl">02.</span>Tidymass</span>
<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a><span class="do">##> 第二步 通过sftp将脚本文件上传到该路径</span></span>
<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a><span class="do">##> 第三步 输入下面代码把脚本写进环境变量，添加alias</span></span>
<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a>echo <span class="st">'alias peakpicking="Rscript ~/01.src/02.script/02.Tidymass/02.PeakPicking.R"'</span> <span class="sc">></span><span class="er">></span> <span class="er">~/</span>.bash_alias</span>
<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a>echo <span class="st">"alias ms1convert='bash ~/01.src/02.script/02.Tidymass/01.msconvert.sh'"</span><span class="sc">></span><span class="er">></span> <span class="er">~/</span>.bash_alias</span>
<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a>echo <span class="st">"alias ms2convert='bash ~/01.src/02.script/02.Tidymass/03.ms2convert.sh'"</span> <span class="sc">></span><span class="er">></span> <span class="er">~/</span>.bash_alias</span>
<span id="cb3-9"><a href="#cb3-9" aria-hidden="true" tabindex="-1"></a>echo <span class="st">"alias runTidymass='bash ~/01.src/02.script/02.Tidymass/runTidymass.sh'"</span> <span class="sc">></span><span class="er">></span> <span class="er">~/</span>.bash_alias</span>
<span id="cb3-10"><a href="#cb3-10" aria-hidden="true" tabindex="-1"></a>echo <span class="st">"alias datacleaning='Rscript ~/01.src/02.script/02.Tidymass/04.dataclean.R'"</span> <span class="sc">></span><span class="er">></span> <span class="er">~/</span>.bash_alias</span>
<span id="cb3-11"><a href="#cb3-11" aria-hidden="true" tabindex="-1"></a>echo <span class="st">"alias feature_anno='Rscript ~/01.src/02.script/02.Tidymass/05.feature_anno'"</span> <span class="sc">></span><span class="er">></span> <span class="er">~/</span>.bash_alias</span>
<span id="cb3-12"><a href="#cb3-12" aria-hidden="true" tabindex="-1"></a>echo <span class="st">"alias feature_downstream='Rscript ~/01.src/02.script/02.Tidymass/06.feature_downstream.R'"</span> <span class="sc">></span><span class="er">></span> <span class="er">~/</span>.bash_alias</span>
<span id="cb3-13"><a href="#cb3-13" aria-hidden="true" tabindex="-1"></a>echo <span class="st">"source ~/.bash_alias"</span> <span class="sc">></span><span class="er">></span> <span class="er">~/</span>.bashrc</span>
<span id="cb3-14"><a href="#cb3-14" aria-hidden="true" tabindex="-1"></a>source <span class="sc">~</span><span class="er">/</span>.bashrc</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>至此分析环境搭建完毕。</p>
</section>
<section id="标准流程" class="level1">
<h1>标准流程：</h1>
<table class="table">
<colgroup>
<col style="width: 20%">
<col style="width: 20%">
<col style="width: 20%">
<col style="width: 20%">
<col style="width: 20%">
</colgroup>
<thead>
<tr class="header">
<th>步骤</th>
<th>描述</th>
<th>脚本名称</th>
<th>状态</th>
<th>改进方向</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>1</td>
<td>下机数据转换为开源格式.mzXML</td>
<td>01.msconvert.sh</td>
<td><font color="green">正常</font></td>
<td>效率较低，优化并行</td>
</tr>
<tr class="even">
<td>2</td>
<td>下机数据转换为开源格式.mgf</td>
<td>03.ms2convert.sh</td>
<td><font color="green">正常</font></td>
<td>效率较低，优化并行</td>
</tr>
<tr class="odd">
<td>3</td>
<td>feature提取</td>
<td>02.PeakPicking.R</td>
<td><font color="green">正常</font></td>
<td>无</td>
</tr>
<tr class="even">
<td>4</td>
<td>数据清洗</td>
<td>04.dataclean.R</td>
<td><font color="green">正常</font></td>
<td>目前没有遇到bug，依据项目改进</td>
</tr>
<tr class="odd">
<td>5</td>
<td>化合物注释，分类</td>
<td>05.feature_anno.R</td>
<td><font color="blue">待优化</font></td>
<td>提高MS1搜库效率，联系Dr. Shen</td>
</tr>
<tr class="even">
<td>6</td>
<td>下游分析</td>
<td>06.feature_downstream.sh</td>
<td><font color="blue">待优化</font></td>
<td>目前包括差异分析，富集分析</td>
</tr>
<tr class="odd">
<td>7</td>
<td>报告生产</td>
<td>07.report.R</td>
<td><font color="red">待启动</font></td>
<td>确定了下游分析对象后自动化生成</td>
</tr>
<tr class="even">
<td>8</td>
<td>一键流程</td>
<td>runTidymass.sh</td>
<td><font color="purple">开发中</font></td>
<td>断点继续的判断</td>
</tr>
<tr class="odd">
<td>9</td>
<td>shinyapp开发</td>
<td>runTidymass_shiny</td>
<td><font color="purple">未启动</font></td>
<td></td>
</tr>
</tbody>
</table>
<section id="标准流程图" class="level2">
<h2 class="anchored" data-anchor-id="标准流程图">标准流程图：</h2>
<p>下面所说的对象为<code>tidymass</code>构建的<code>S4</code>对象,被称为<code>massdataset</code>，其中包含了所有<code>feature</code>的质谱信息、表达水平、测试材料信息等。</p>
<div class="cell">
<div class="cell-output-display">
<div>
<p>
</p><pre class="mermaid mermaid-js" data-tooltip-selector="#mermaid-tooltip-1">flowchart TB
A[下机原始数据] -- 01.msconvert.sh --> B[开源格式.mzXML]
A[下机原始数据.raw] -- 03.ms2convert.sh --> C[开源格式.mgf]
B[开源格式.mzXML] -- 02.PeakPicking.R --> D[原始对象]
D[初始对象] -- 04.dataclean.R --> E[过滤后对象]
E[过滤后对象] -- 05.feature_anno.R --> F[注释后对象]
C[开源格式.mgf] -- 05.feature_anno.R --> F[注释后对象]
F[注释后对象] --06.feature_downstream.sh --> G[下游分析]
G[下游分析] --07.report.R --> H[生成报告]
</pre>
<div id="mermaid-tooltip-1" class="mermaidTooltip">
</div>
<p></p>
</div>
</div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="sc">--------------------</span> </span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>massdataset version<span class="sc">:</span> <span class="dv">1</span>.<span class="fl">0.5</span> </span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a><span class="sc">--------------------</span> </span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a><span class="fl">1.</span>expression_data<span class="sc">:</span>[ <span class="dv">5105</span> x <span class="dv">244</span> data.frame]</span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a><span class="fl">2.</span>sample_info<span class="sc">:</span>[ <span class="dv">244</span> x <span class="dv">4</span> data.frame]</span>
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a><span class="fl">3.</span>variable_info<span class="sc">:</span>[ <span class="dv">5105</span> x <span class="dv">3</span> data.frame]</span>
<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a><span class="fl">4.</span>sample_info_note<span class="sc">:</span>[ <span class="dv">4</span> x <span class="dv">2</span> data.frame]</span>
<span id="cb4-8"><a href="#cb4-8" aria-hidden="true" tabindex="-1"></a><span class="fl">5.</span>variable_info_note<span class="sc">:</span>[ <span class="dv">3</span> x <span class="dv">2</span> data.frame]</span>
<span id="cb4-9"><a href="#cb4-9" aria-hidden="true" tabindex="-1"></a><span class="fl">6.</span>ms2_data<span class="sc">:</span>[ <span class="dv">0</span> variables x <span class="dv">0</span> MS2 spectra]</span>
<span id="cb4-10"><a href="#cb4-10" aria-hidden="true" tabindex="-1"></a><span class="sc">--------------------</span> </span>
<span id="cb4-11"><a href="#cb4-11" aria-hidden="true" tabindex="-1"></a>Processing <span class="fu">information</span> (<span class="fu">extract_process_info</span>())</span>
<span id="cb4-12"><a href="#cb4-12" aria-hidden="true" tabindex="-1"></a><span class="dv">2</span> processings <span class="cf">in</span> total</span>
<span id="cb4-13"><a href="#cb4-13" aria-hidden="true" tabindex="-1"></a>create_mass_dataset <span class="sc">----------</span> </span>
<span id="cb4-14"><a href="#cb4-14" aria-hidden="true" tabindex="-1"></a> Package Function.used Time</span>
<span id="cb4-15"><a href="#cb4-15" aria-hidden="true" tabindex="-1"></a><span class="dv">1</span> massdataset <span class="fu">create_mass_dataset</span>() <span class="dv">2022-12-06</span> <span class="dv">08</span><span class="sc">:</span><span class="dv">50</span><span class="sc">:</span><span class="dv">25</span></span>
<span id="cb4-16"><a href="#cb4-16" aria-hidden="true" tabindex="-1"></a>process_data <span class="sc">----------</span> </span>
<span id="cb4-17"><a href="#cb4-17" aria-hidden="true" tabindex="-1"></a> Package Function.used Time</span>
<span id="cb4-18"><a href="#cb4-18" aria-hidden="true" tabindex="-1"></a><span class="dv">1</span> massprocesser process_data <span class="dv">2022-12-06</span> <span class="dv">08</span><span class="sc">:</span><span class="dv">32</span><span class="sc">:</span><span class="dv">23</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="使用方法" class="level2">
<h2 class="anchored" data-anchor-id="使用方法">使用方法</h2>
<section id="数据准备" class="level3">
<h3 class="anchored" data-anchor-id="数据准备">数据准备</h3>
<ul>
<li><p>在实验准备前，先对样品进行编号匹配，样品编号统一为<code>S_0001 --> S_1000</code>类型，注意这里需要用<code>0</code>补齐,因为linux系统下默认按文件名排序，如果不加<code>pad</code>顺序会是<code>S_1 S_10 S_11 .... S_2 S_20 S_21...</code>造成不必要的错误。<code>pad</code>数量根据样本量的大小补充，三位数补充两位，四位数补充3位。同样<code>QC</code>编号为<code>QC_01 ... QC_20</code>;</p></li>
<li><p>文件结构,对于正负谱同时采的项目，将所有<code>.raw</code>文件放到一个文件夹下，用<code>bio</code>账号拷贝到<code>/home/data/public/02.rawdata/03.Metabolomics/kq-1</code>路径下。</p></li>
<li><p>文件结构,对于正负谱分开采的项目，首先新建两个文件夹，一个为<code>NEG</code>,另一个位<code>POS</code>,分别将正负谱的结果放入对应的文件夹，然后拷贝。</p></li>
</ul>
<div class="cell">
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>shawn<span class="sc">@</span>bio<span class="sc">-</span>Super<span class="sc">-</span>Server<span class="sc">:</span><span class="er">~/</span>public<span class="sc">/</span><span class="fl">02.</span>rawdata<span class="sc">/</span><span class="fl">03.</span>Metabolomics<span class="sc">$</span> tree <span class="sc">-</span>d kq<span class="dv">-1</span></span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>kq<span class="dv">-1</span></span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a><span class="sc">|</span>___ NEG</span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a><span class="sc">|</span>___ POS</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>必须严格按照命名规则和文件格式准备，<code>QC, S, NEG, POS</code>均为大写，<code>_</code>为下划线。</p>
</section>
<section id="脚本运行" class="level3">
<h3 class="anchored" data-anchor-id="脚本运行">脚本运行</h3>
<p>目前一键运行脚本已经开发到全部完成<code>1-4</code>步骤,并且具有断点续跑的功能。所以可以通过<code>runTidymass.sh</code>进行<code>1-4</code>步骤。</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="sc">/</span>home<span class="sc">/</span>data<span class="sc">/</span>shawn<span class="sc">/</span><span class="fl">01.</span>src<span class="sc">/</span><span class="fl">02.</span>script<span class="sc">/</span><span class="fl">02.</span>Tidymass<span class="sc">/</span>runTidymass.sh<span class="sc">:</span> option requires an argument <span class="sc">--</span> h</span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>Tidymass pipeline part1. Date transform and peak picking</span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a><span class="sc">@</span>Usage<span class="sc">:</span></span>
<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a><span class="sc">-------------------------------</span></span>
<span id="cb6-6"><a href="#cb6-6" aria-hidden="true" tabindex="-1"></a>runTidymass [<span class="sc">-</span>i input] [<span class="sc">-</span>t type] [<span class="sc">-</span>c column]</span>
<span id="cb6-7"><a href="#cb6-7" aria-hidden="true" tabindex="-1"></a><span class="sc">-------------------------------</span></span>
<span id="cb6-8"><a href="#cb6-8" aria-hidden="true" tabindex="-1"></a><span class="er">@</span>Author Shawn <span class="fu">Wang</span> (shawnwang2016<span class="sc">@</span><span class="fl">126.</span>com)</span>
<span id="cb6-9"><a href="#cb6-9" aria-hidden="true" tabindex="-1"></a><span class="sc">-------------------------------</span></span>
<span id="cb6-10"><a href="#cb6-10" aria-hidden="true" tabindex="-1"></a><span class="er">@</span>Date Tus Feb <span class="dv">09</span>, <span class="dv">2023</span></span>
<span id="cb6-11"><a href="#cb6-11" aria-hidden="true" tabindex="-1"></a><span class="sc">-------------------------------</span></span>
<span id="cb6-12"><a href="#cb6-12" aria-hidden="true" tabindex="-1"></a><span class="er">@</span>Version V.<span class="dv">0</span>.<span class="dv">0</span>.<span class="fl">0.99</span> beta</span>
<span id="cb6-13"><a href="#cb6-13" aria-hidden="true" tabindex="-1"></a><span class="sc">-------------------------------</span></span>
<span id="cb6-14"><a href="#cb6-14" aria-hidden="true" tabindex="-1"></a><span class="er">@</span>Description</span>
<span id="cb6-15"><a href="#cb6-15" aria-hidden="true" tabindex="-1"></a><span class="sc">-------------------------------</span></span>
<span id="cb6-16"><a href="#cb6-16" aria-hidden="true" tabindex="-1"></a>[<span class="sc">-</span>i]<span class="sc">:</span>input, The file path of .raw data</span>
<span id="cb6-17"><a href="#cb6-17" aria-hidden="true" tabindex="-1"></a>[<span class="sc">-</span>t]<span class="sc">:</span>type, The type of ion model, <span class="dv">1</span><span class="sc">:</span> NEG<span class="sc">+</span>POS <span class="cf">in</span> one file, <span class="dv">2</span><span class="sc">:</span> NEG and POS <span class="cf">in</span> differnet files</span>
<span id="cb6-18"><a href="#cb6-18" aria-hidden="true" tabindex="-1"></a>[<span class="sc">-</span>c]<span class="sc">:</span>column, rp or hilic</span>
<span id="cb6-19"><a href="#cb6-19" aria-hidden="true" tabindex="-1"></a><span class="sc">-------------------------------</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>目前需要的参数：</p>
<p><font color="green"><strong>-i | input</strong></font>：原始数据存放路径，一般为在<code>/home/data/public/02.rawdata/03.Metabolomics/xxx</code>。</p>
<p><font color="green"><strong>-t | type</strong></font>：采集模式，1：为正负谱同时采集，2：正负谱分开采集。</p>
<p><font color="green"><strong>-c | column</strong></font>：柱子型号，rp 还是 hilic。</p>
</section>
<section id="输出结果文件结构" class="level3">
<h3 class="anchored" data-anchor-id="输出结果文件结构">输出结果文件结构</h3>
<div class="cell">
<div class="sourceCode cell-code" id="cb7"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>shawn<span class="sc">@</span>bio<span class="sc">-</span>Super<span class="sc">-</span>Server<span class="sc">:</span><span class="er">~/</span><span class="fl">02.</span>project<span class="sc">/</span><span class="fl">13.</span>kq1<span class="sc">$</span> tree <span class="sc">-</span>d test<span class="sc">/</span></span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a>test<span class="sc">/</span></span>
<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a>└── working_dir</span>
<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a> ├── <span class="fl">01.</span>data</span>
<span id="cb7-5"><a href="#cb7-5" aria-hidden="true" tabindex="-1"></a> │ └── rawdata</span>
<span id="cb7-6"><a href="#cb7-6" aria-hidden="true" tabindex="-1"></a> │ ├── NEG</span>
<span id="cb7-7"><a href="#cb7-7" aria-hidden="true" tabindex="-1"></a> │ │ ├── QC</span>
<span id="cb7-8"><a href="#cb7-8" aria-hidden="true" tabindex="-1"></a> │ │ └── Subject</span>
<span id="cb7-9"><a href="#cb7-9" aria-hidden="true" tabindex="-1"></a> │ └── POS</span>
<span id="cb7-10"><a href="#cb7-10" aria-hidden="true" tabindex="-1"></a> │ ├── QC</span>
<span id="cb7-11"><a href="#cb7-11" aria-hidden="true" tabindex="-1"></a> │ └── Subject</span>
<span id="cb7-12"><a href="#cb7-12" aria-hidden="true" tabindex="-1"></a> ├── <span class="fl">02.</span>progress</span>
<span id="cb7-13"><a href="#cb7-13" aria-hidden="true" tabindex="-1"></a> │ ├── Data_cleaning</span>
<span id="cb7-14"><a href="#cb7-14" aria-hidden="true" tabindex="-1"></a> │ ├── annotation</span>
<span id="cb7-15"><a href="#cb7-15" aria-hidden="true" tabindex="-1"></a> │ ├── peak_picking</span>
<span id="cb7-16"><a href="#cb7-16" aria-hidden="true" tabindex="-1"></a> │ │ ├── NEG</span>
<span id="cb7-17"><a href="#cb7-17" aria-hidden="true" tabindex="-1"></a> │ │ │ └── Result</span>
<span id="cb7-18"><a href="#cb7-18" aria-hidden="true" tabindex="-1"></a> │ │ │ └── intermediate_data</span>
<span id="cb7-19"><a href="#cb7-19" aria-hidden="true" tabindex="-1"></a> │ │ └── POS</span>
<span id="cb7-20"><a href="#cb7-20" aria-hidden="true" tabindex="-1"></a> │ │ └── Result</span>
<span id="cb7-21"><a href="#cb7-21" aria-hidden="true" tabindex="-1"></a> │ │ └── intermediate_data</span>
<span id="cb7-22"><a href="#cb7-22" aria-hidden="true" tabindex="-1"></a> │ └── transform</span>
<span id="cb7-23"><a href="#cb7-23" aria-hidden="true" tabindex="-1"></a> │ ├── MS1</span>
<span id="cb7-24"><a href="#cb7-24" aria-hidden="true" tabindex="-1"></a> │ │ ├── NEG</span>
<span id="cb7-25"><a href="#cb7-25" aria-hidden="true" tabindex="-1"></a> │ │ │ ├── QC</span>
<span id="cb7-26"><a href="#cb7-26" aria-hidden="true" tabindex="-1"></a> │ │ │ └── Subject</span>
<span id="cb7-27"><a href="#cb7-27" aria-hidden="true" tabindex="-1"></a> │ │ └── POS</span>
<span id="cb7-28"><a href="#cb7-28" aria-hidden="true" tabindex="-1"></a> │ │ ├── QC</span>
<span id="cb7-29"><a href="#cb7-29" aria-hidden="true" tabindex="-1"></a> │ │ └── Subject</span>
<span id="cb7-30"><a href="#cb7-30" aria-hidden="true" tabindex="-1"></a> │ └── MS2</span>
<span id="cb7-31"><a href="#cb7-31" aria-hidden="true" tabindex="-1"></a> │ ├── NEG</span>
<span id="cb7-32"><a href="#cb7-32" aria-hidden="true" tabindex="-1"></a> │ │ ├── QC</span>
<span id="cb7-33"><a href="#cb7-33" aria-hidden="true" tabindex="-1"></a> │ │ └── Subject</span>
<span id="cb7-34"><a href="#cb7-34" aria-hidden="true" tabindex="-1"></a> │ └── POS</span>
<span id="cb7-35"><a href="#cb7-35" aria-hidden="true" tabindex="-1"></a> │ ├── QC</span>
<span id="cb7-36"><a href="#cb7-36" aria-hidden="true" tabindex="-1"></a> │ └── Subject</span>
<span id="cb7-37"><a href="#cb7-37" aria-hidden="true" tabindex="-1"></a> └── <span class="fl">03.</span>result</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
</section>
</section>
<section id="目前的问题" class="level1">
<h1>目前的问题：</h1>
<p>Q1. 格式转换速度比较慢，目前搞清楚的问题来源是通过<code>docker</code>运行<code>msconvert</code>不同同时处理多个原始数据文件。</p>
<p>M1. 尝试并行，准备好原始数据后迭代，但可能开大量虚拟机对服务器负载要求较高。第二个方案是在windows下直接用<code>msconvert</code>转换，这种方法可以同时转换大量原始数据。</p>
<p>Q2. 正负谱同时采集的数据用tidymass提峰结果又很大问题。目前原因不明，需要进一步检查结果</p>
</section>
<section id="计划" class="level1">
<h1>计划</h1>
<ol type="1">
<li><p>本周完成下游分析脚本调试。</p></li>
<li><p>下周3之前完成一键脚本流程的调试，投入使用。</p></li>
<li><p>5周内完成shinyapp开发，文章写作。</p></li>
</ol>
</section>
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});
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}
});
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