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    <meta name="description" content="通过比对，我们得到了counts矩阵，接下来可以进行DEGs分析。此时如果我们有多组之间的对比，则可以使用RRA算法来聚合我们的结果。RRA的安装过程见此。 第一步，多组差异基因分析1234567891011121314151617181920212223242526272829303132333435library(DESeq2)count_all &lt;- read.csv(&quot;~&#x2F;">
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<meta property="og:description" content="通过比对，我们得到了counts矩阵，接下来可以进行DEGs分析。此时如果我们有多组之间的对比，则可以使用RRA算法来聚合我们的结果。RRA的安装过程见此。 第一步，多组差异基因分析1234567891011121314151617181920212223242526272829303132333435library(DESeq2)count_all &lt;- read.csv(&quot;~&#x2F;">
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            <h1 id="seo-header">从差异基因到RRA聚合</h1>
            
            
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                <p>通过<a href="https://occdn.limour.top/1934.html">比对</a>，我们得到了counts矩阵，接下来可以进行DEGs分析。此时如果我们有多组之间的对比，则可以使用<a href="https://occdn.limour.top/1658.html">RRA算法</a>来聚合我们的结果。<a href="https://occdn.limour.top/1653.html">RRA的安装过程见此</a>。</p>
<h2 id="第一步，多组差异基因分析"><a href="#第一步，多组差异基因分析" class="headerlink" title="第一步，多组差异基因分析"></a>第一步，多组差异基因分析</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><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>DESeq2<span class="hljs-punctuation">)</span><br>count_all <span class="hljs-operator">&lt;-</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;~/upload/zl_liu/star_data/yyz_01/yyz_01.csv&quot;</span><span class="hljs-punctuation">,</span>header<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br>count_all<br>cts_b <span class="hljs-operator">&lt;-</span> count_all<span class="hljs-punctuation">[</span> <span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-operator">-</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-operator">-</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>rownames<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> count_all<span class="hljs-operator">$</span>ID<br>keep <span class="hljs-operator">&lt;-</span> rowSums<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">)</span> <span class="hljs-operator">&gt;</span> ncol<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">)</span><br>cts_b<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>f_DESeq2 <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>cts_bb<span class="hljs-punctuation">,</span> rowInfo<span class="hljs-punctuation">,</span> ControlN<span class="hljs-punctuation">,</span> TreatN<span class="hljs-punctuation">,</span> rm.NA<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    cts_b <span class="hljs-operator">&lt;-</span> cts_bb<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>ControlN<span class="hljs-punctuation">,</span> TreatN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>    conditions <span class="hljs-operator">&lt;-</span> factor<span class="hljs-punctuation">(</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Control&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>ControlN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Treat&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>TreatN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <br>    colData_b <span class="hljs-operator">&lt;-</span> data.frame<span class="hljs-punctuation">(</span>row.names <span class="hljs-operator">=</span> colnames<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> conditions<span class="hljs-punctuation">)</span><br>    print<span class="hljs-punctuation">(</span>colData_b<span class="hljs-punctuation">)</span><br>    dds <span class="hljs-operator">&lt;-</span> DESeqDataSetFromMatrix<span class="hljs-punctuation">(</span>countData <span class="hljs-operator">=</span> cts_b<span class="hljs-punctuation">,</span><br>                              colData <span class="hljs-operator">=</span> colData_b<span class="hljs-punctuation">,</span><br>                              design <span class="hljs-operator">=</span> <span class="hljs-operator">~</span> conditions<span class="hljs-punctuation">)</span><br>    dds <span class="hljs-operator">&lt;-</span> DESeq<span class="hljs-punctuation">(</span>dds<span class="hljs-punctuation">)</span><br>    res <span class="hljs-operator">&lt;-</span> results<span class="hljs-punctuation">(</span>dds<span class="hljs-punctuation">)</span><br>    rres <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>rowInfo<span class="hljs-punctuation">,</span> data.frame<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>rm.NA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span>rres <span class="hljs-operator">&lt;-</span> rres<span class="hljs-punctuation">[</span><span class="hljs-operator">!</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>rres<span class="hljs-operator">$</span>padj<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">&#125;</span><br>    rres <span class="hljs-operator">&lt;-</span> rres<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>rres<span class="hljs-operator">$</span>log2FoldChange<span class="hljs-punctuation">,</span> decreasing <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>    saveRDS<span class="hljs-punctuation">(</span>rres<span class="hljs-punctuation">,</span> paste<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;DEGs&#x27;</span><span class="hljs-punctuation">,</span> paste<span class="hljs-punctuation">(</span>TreatN<span class="hljs-punctuation">,</span> collapse <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;_&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;vs.&#x27;</span><span class="hljs-punctuation">,</span> paste<span class="hljs-punctuation">(</span>ControlN<span class="hljs-punctuation">,</span> collapse <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;_&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;DESeq2.rds&#x27;</span><span class="hljs-punctuation">,</span>sep <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;_&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    rres<br><span class="hljs-punctuation">&#125;</span><br>Ct1 <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;X1.control.DMSO&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;X2.control.DMSO&#x27;</span><span class="hljs-punctuation">)</span><br>Tt1 <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;X1.OE.DMSO&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;X2.OE.DMSO&#x27;</span><span class="hljs-punctuation">)</span><br>Ct2 <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;X1.OE.DMSO&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;X2.OE.DMSO&#x27;</span><span class="hljs-punctuation">)</span><br>Tt2 <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;X1.OE.Enz&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;X2.OE.Enz&#x27;</span><span class="hljs-punctuation">)</span><br>Ct3 <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;X1.control.Enz&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;X2.control.Enz&#x27;</span><span class="hljs-punctuation">)</span><br>Tt3 <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;X1.OE.Enz&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;X2.OE.Enz&#x27;</span><span class="hljs-punctuation">)</span><br>Ct4 <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;X1.CAF.DMSO&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;X2.CAF.DMSO&#x27;</span><span class="hljs-punctuation">)</span><br>Tt4 <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;X1.CAF.Enz&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;X2.CAF.Enz&#x27;</span><span class="hljs-punctuation">)</span><br>r1 <span class="hljs-operator">&lt;-</span> f_DESeq2<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> count_all<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> Ct1<span class="hljs-punctuation">,</span> Tt1<span class="hljs-punctuation">)</span><br>r2 <span class="hljs-operator">&lt;-</span> f_DESeq2<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> count_all<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> Ct2<span class="hljs-punctuation">,</span> Tt2<span class="hljs-punctuation">)</span><br>r3 <span class="hljs-operator">&lt;-</span> f_DESeq2<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> count_all<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> Ct3<span class="hljs-punctuation">,</span> Tt3<span class="hljs-punctuation">)</span><br>r4 <span class="hljs-operator">&lt;-</span> f_DESeq2<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> count_all<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> Ct4<span class="hljs-punctuation">,</span> Tt4<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="第二步，RRA聚合差异结果"><a href="#第二步，RRA聚合差异结果" class="headerlink" title="第二步，RRA聚合差异结果"></a>第二步，RRA聚合差异结果</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><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br></pre></td><td class="code"><pre><code class="hljs R">require<span class="hljs-punctuation">(</span>RobustRankAggreg<span class="hljs-punctuation">)</span><br>f_dflist_RRA <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>dflist<span class="hljs-punctuation">,</span> nameN<span class="hljs-punctuation">,</span> N<span class="hljs-punctuation">,</span> orderN<span class="hljs-punctuation">,</span> decreasing<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    res <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>name <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>dflist<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        tmp <span class="hljs-operator">&lt;-</span> dflist<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>        <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span>nrow<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span> <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            res<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> nameN<span class="hljs-punctuation">]</span><br>        <span class="hljs-punctuation">&#125;</span><span class="hljs-keyword">else</span> <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>nrow<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span> <span class="hljs-operator">&gt;=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            res<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">[[</span>orderN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>decreasing <span class="hljs-operator">=</span> decreasing<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> nameN<span class="hljs-punctuation">]</span><br>        <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span> <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#125;</span><br>    aggregateRanks<span class="hljs-punctuation">(</span>glist <span class="hljs-operator">=</span> res<span class="hljs-punctuation">,</span> N <span class="hljs-operator">=</span> N<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>rownames<span class="hljs-punctuation">(</span>count_all<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> count_all<span class="hljs-operator">$</span>ID<br> <br>r <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>r1<span class="hljs-operator">=</span>r1<span class="hljs-punctuation">,</span>r2<span class="hljs-operator">=</span>r2<span class="hljs-punctuation">,</span>r3<span class="hljs-operator">=</span>r3<span class="hljs-punctuation">,</span>r4<span class="hljs-operator">=</span>r4<span class="hljs-punctuation">)</span><br>r <span class="hljs-operator">&lt;-</span> lapply<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> FUN <span class="hljs-operator">=</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span>subset<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">,</span> padj<span class="hljs-operator">&lt;</span><span class="hljs-number">0.05</span> <span class="hljs-operator">&amp;</span> log2FoldChange <span class="hljs-operator">&gt;</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">)</span><br>r <span class="hljs-operator">&lt;-</span> f_dflist_RRA<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;ID&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>keep<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;log2FoldChange&#x27;</span><span class="hljs-punctuation">)</span><br>r <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>count_all<span class="hljs-punctuation">[</span>r<span class="hljs-operator">$</span>Name<span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> r<span class="hljs-punctuation">)</span><br>r<br>write.csv<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;RRA_up.csv&#x27;</span><span class="hljs-punctuation">)</span><br> <br>r <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>r1<span class="hljs-operator">=</span>r1<span class="hljs-punctuation">,</span>r2<span class="hljs-operator">=</span>r2<span class="hljs-punctuation">,</span>r3<span class="hljs-operator">=</span>r3<span class="hljs-punctuation">,</span>r4<span class="hljs-operator">=</span>r4<span class="hljs-punctuation">)</span><br>r <span class="hljs-operator">&lt;-</span> lapply<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> FUN <span class="hljs-operator">=</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span>subset<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">,</span> padj<span class="hljs-operator">&lt;</span><span class="hljs-number">0.05</span> <span class="hljs-operator">&amp;</span> log2FoldChange <span class="hljs-operator">&lt;</span> <span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">)</span><br>r <span class="hljs-operator">&lt;-</span> f_dflist_RRA<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;ID&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>keep<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;log2FoldChange&#x27;</span><span class="hljs-punctuation">,</span> decreasing <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br>r <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>count_all<span class="hljs-punctuation">[</span>r<span class="hljs-operator">$</span>Name<span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> r<span class="hljs-punctuation">)</span><br>r<br>write.csv<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;RRA_down.csv&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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  Fluid.utils.createScript('https://jscdn.limour.top/npm/anchor-js@4.3.1/anchor.min.js', function() {
    window.anchors.options = {
      placement: CONFIG.anchorjs.placement,
      visible  : CONFIG.anchorjs.visible
    };
    if (CONFIG.anchorjs.icon) {
      window.anchors.options.icon = CONFIG.anchorjs.icon;
    }
    var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
    var res = [];
    for (var item of el) {
      res.push('.markdown-body > ' + item.trim());
    }
    if (CONFIG.anchorjs.placement === 'left') {
      window.anchors.options.class = 'anchorjs-link-left';
    }
    window.anchors.add(res.join(', '));

    Fluid.events.registerRefreshCallback(function() {
      if ('anchors' in window) {
        anchors.removeAll();
        var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
        var res = [];
        for (var item of el) {
          res.push('.markdown-body > ' + item.trim());
        }
        if (CONFIG.anchorjs.placement === 'left') {
          anchors.options.class = 'anchorjs-link-left';
        }
        anchors.add(res.join(', '));
      }
    });
  });
</script>


<script>
  Fluid.utils.createScript('https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.js', function() {
    Fluid.plugins.fancyBox();
  });
</script>


  <script>Fluid.plugins.imageCaption();</script>

  <script  src="/js/local-search.js" ></script>


<!-- 主题的启动项，将它保持在最底部 -->
<!-- the boot of the theme, keep it at the bottom -->
<script  src="/js/boot.js" ></script>


  <noscript>
    <div class="noscript-warning">Blog works best with JavaScript enabled</div>
  </noscript>
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  <script defer src="/theme-inject/timeliness.js"></script>
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</html>