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            <span id="subtitle">【迁移】使用 JTK_CYCLE 算法分析生物节律</span>
          
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            <h1 id="seo-header">【迁移】使用 JTK_CYCLE 算法分析生物节律</h1>
            
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                    Last updated on March 19, 2024 pm
                  
                
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                <p>JTK是一种非参数检测程序，能从芯片数据中检测循环转录本。除了计算每个转录本最佳的相位(LAG)、振幅(AMP)和周期(PER)外，JTK还计算了置换检验P值(ADJ.P)和Benjamini-Hochberg q值 (BH.Q)。与常规的周期检测算法相比，JTK具有更好的检验效能、更高的计算效率和更强的鲁棒性。R语言的<strong>metacycle</strong>包实现了<strong>ARSER</strong>、<strong>JTK_CYCLE</strong>、<strong>Lomb-Scargle</strong>三种分析方法。</p>
<h2 id="conda安装包">conda安装包</h2>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br></pre></td><td class="code"><pre><code class="hljs bash">conda create -n metacycle -c conda-forge r-base=4.1.3<br>conda activate metacycle<br>conda install -c conda-forge r-metacycle -y<br>conda install -c conda-forge r-cosinor -y<br>conda install -c conda-forge r-tidyverse -y<br>conda install -c conda-forge r-irkernel -y<br>Rscript -e <span class="hljs-string">&quot;IRkernel::installspec(name=&#x27;metacycle&#x27;, displayname=&#x27;r-metacycle&#x27;)&quot;</span><br>install.packages(<span class="hljs-string">&#x27;cosinor2&#x27;</span>)<br></code></pre></td></tr></table></figure>
<h2 id="准备数据">准备数据</h2>
<p>通过<a href="/STAR--yi-jian-jiao-ben">比对</a>，得到的counts矩阵</p>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br></pre></td><td class="code"><pre><code class="hljs R">require<span class="hljs-punctuation">(</span>MetaCycle<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>tidyverse<span class="hljs-punctuation">)</span><br>tmp <span class="hljs-operator">&lt;-</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;zctcount.csv&#x27;</span><span class="hljs-punctuation">,</span> row.names <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>head<span class="hljs-punctuation">(</span>cycMouseLiverRNA<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">5</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>tmp <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-punctuation">[</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;ID&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;ZT16.con.1&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;ZT16.con.2&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;ZT16.con.3&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;ZT16.con.4&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;ZT28.con.1&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;ZT28.con.2&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;ZT28.con.3&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;ZT28.con.4&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>write.csv<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">,</span> file<span class="hljs-operator">=</span><span class="hljs-string">&quot;tmp.csv&quot;</span><span class="hljs-punctuation">,</span> row.names<span class="hljs-operator">=</span><span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<p><a href="/Counts-ju-zhen-de-biao-zhun-hua-fang-fa--TMM-he-VST-RLOG">f_counts2TMM</a></p>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><code class="hljs R">tmp <span class="hljs-operator">&lt;-</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;tmp.csv&#x27;</span><span class="hljs-punctuation">,</span> row.names <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>tmp <span class="hljs-operator">&lt;-</span> f_counts2TMM<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><br>tmp <span class="hljs-operator">&lt;-</span> log2<span class="hljs-punctuation">(</span>tmp <span class="hljs-operator">+</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>write.csv<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">,</span> file<span class="hljs-operator">=</span><span class="hljs-string">&quot;tmp.csv&quot;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<h2 id="分析周期节律">分析周期节律</h2>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><code class="hljs R">meta2d<span class="hljs-punctuation">(</span>infile<span class="hljs-operator">=</span><span class="hljs-string">&quot;tmp.csv&quot;</span><span class="hljs-punctuation">,</span>filestyle<span class="hljs-operator">=</span><span class="hljs-string">&quot;csv&quot;</span><span class="hljs-punctuation">,</span>outdir<span class="hljs-operator">=</span><span class="hljs-string">&quot;example&quot;</span><span class="hljs-punctuation">,</span> cycMethod<span class="hljs-operator">=</span><span class="hljs-string">&quot;JTK&quot;</span><span class="hljs-punctuation">,</span> timepoints<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">16</span><span class="hljs-punctuation">,</span><span class="hljs-number">16</span><span class="hljs-punctuation">,</span><span class="hljs-number">16</span><span class="hljs-punctuation">,</span><span class="hljs-number">16</span><span class="hljs-punctuation">,</span><span class="hljs-number">28</span><span class="hljs-punctuation">,</span><span class="hljs-number">28</span><span class="hljs-punctuation">,</span><span class="hljs-number">28</span><span class="hljs-punctuation">,</span><span class="hljs-number">28</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>outRawData<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br>r1 <span class="hljs-operator">&lt;-</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;example/JTKresult_tmp.csv&#x27;</span><span class="hljs-punctuation">)</span><br>r2 <span class="hljs-operator">&lt;-</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;example/meta2d_tmp.csv&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<h2 id="绘制热图">绘制热图</h2>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br></pre></td><td class="code"><pre><code class="hljs R">require<span class="hljs-punctuation">(</span>pheatmap<span class="hljs-punctuation">)</span><br>r1 <span class="hljs-operator">&lt;-</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;example/JTKresult_tmp.csv&#x27;</span><span class="hljs-punctuation">)</span><br>r1 <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>r1<span class="hljs-punctuation">,</span> ADJ.P <span class="hljs-operator">&lt;</span> <span class="hljs-number">0.1</span><span class="hljs-punctuation">)</span><br>dat <span class="hljs-operator">&lt;-</span> r1<span class="hljs-punctuation">[</span><span class="hljs-operator">-</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">6</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>p3 <span class="hljs-operator">&lt;-</span> pheatmap<span class="hljs-punctuation">(</span>dat<span class="hljs-punctuation">,</span> scale <span class="hljs-operator">=</span> <span class="hljs-string">&quot;row&quot;</span><span class="hljs-punctuation">,</span> cluster_cols <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span><br>  border_color <span class="hljs-operator">=</span> <span class="hljs-literal">NA</span><span class="hljs-punctuation">,</span> show_rownames <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span>treeheight_row <span class="hljs-operator">=</span> <span class="hljs-number">0</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<h2 id="绘制某个基因的拟合曲线">绘制某个基因的拟合曲线</h2>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br></pre></td><td class="code"><pre><code class="hljs R">get_sin_lm <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>PER<span class="hljs-punctuation">,</span> LAG<span class="hljs-punctuation">,</span> AMP<span class="hljs-punctuation">,</span> mean<span class="hljs-operator">=</span><span class="hljs-number">0</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>xvar<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        <span class="hljs-operator">-</span><span class="hljs-punctuation">(</span>AMP<span class="hljs-operator">/</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">*</span> <span class="hljs-built_in">cos</span><span class="hljs-punctuation">(</span><span class="hljs-number">2</span> <span class="hljs-operator">*</span> <span class="hljs-built_in">pi</span><span class="hljs-operator">*</span> <span class="hljs-punctuation">(</span><span class="hljs-punctuation">(</span>xvar <span class="hljs-operator">+</span> LAG<span class="hljs-punctuation">)</span><span class="hljs-operator">/</span>PER<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> mean<br>    <span class="hljs-punctuation">&#125;</span><br><span class="hljs-punctuation">&#125;</span><br>dat <span class="hljs-operator">&lt;-</span> r1<span class="hljs-punctuation">[</span><span class="hljs-operator">-</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">6</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>dat <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>t<span class="hljs-punctuation">(</span>dat<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>colnames<span class="hljs-punctuation">(</span>dat<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> r1<span class="hljs-operator">$</span>CycID<br>index <span class="hljs-operator">=</span> <span class="hljs-number">5</span><br>a <span class="hljs-operator">&lt;-</span> get_sin_lm<span class="hljs-punctuation">(</span>r1<span class="hljs-operator">$</span>PER<span class="hljs-punctuation">[[</span>index<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> r1<span class="hljs-operator">$</span>LAG<span class="hljs-punctuation">[[</span>index<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> r1<span class="hljs-operator">$</span>AMP<span class="hljs-punctuation">[[</span>index<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> mean <span class="hljs-operator">=</span> mean<span class="hljs-punctuation">(</span>unlist<span class="hljs-punctuation">(</span>r1<span class="hljs-punctuation">[</span>index<span class="hljs-punctuation">,</span><span class="hljs-operator">-</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">6</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>mean<span class="hljs-punctuation">(</span>unlist<span class="hljs-punctuation">(</span>r1<span class="hljs-punctuation">[</span>index<span class="hljs-punctuation">,</span><span class="hljs-operator">-</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">6</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>dat1 <span class="hljs-operator">&lt;-</span> dat<span class="hljs-punctuation">[</span>index<span class="hljs-punctuation">]</span><br>dat1<span class="hljs-operator">$</span>x  <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">16</span><span class="hljs-punctuation">,</span><span class="hljs-number">16</span><span class="hljs-punctuation">,</span><span class="hljs-number">16</span><span class="hljs-punctuation">,</span><span class="hljs-number">16</span><span class="hljs-punctuation">,</span><span class="hljs-number">28</span><span class="hljs-punctuation">,</span><span class="hljs-number">28</span><span class="hljs-punctuation">,</span><span class="hljs-number">28</span><span class="hljs-punctuation">,</span><span class="hljs-number">28</span><span class="hljs-punctuation">)</span><br><span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>dat1<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;y&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;x&#x27;</span><span class="hljs-punctuation">)</span><br>ggplot<span class="hljs-punctuation">(</span>dat1<span class="hljs-punctuation">,</span> aes<span class="hljs-punctuation">(</span>x<span class="hljs-operator">=</span>x<span class="hljs-punctuation">,</span> y <span class="hljs-operator">=</span> y<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span><br>stat_function<span class="hljs-punctuation">(</span>fun <span class="hljs-operator">=</span> a<span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> geom_point<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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