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            <h1 id="seo-header">【迁移】从差异基因到RRA聚合</h1>
            
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                    Last updated on March 19, 2024 pm
                  
                
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                <p>通过<a href="/STAR--yi-jian-jiao-ben">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RRA算法来聚合我们的结果。</p>
<h2 id="RRA的安装">RRA的安装</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><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></pre></td><td class="code"><pre><span class="line">conda create -n tcga -c conda-forge r-base=4.1.2 -y</span><br><span class="line">conda activate tcga</span><br><span class="line">conda install -c conda-forge r-rvest=1.0.2 -y</span><br><span class="line">conda install -c conda-forge r-xml=3.99_0.8 -y</span><br><span class="line">conda install -c conda-forge r-rcpparmadillo=0.10.8.1.0 -y</span><br><span class="line">conda install -c conda-forge r-bh=1.78.0_0 -y</span><br><span class="line">conda install -c conda-forge r-biocmanager=1.30.16 -y</span><br><span class="line">conda install -c bioconda bioconductor-summarizedexperiment=1.24.0 -y</span><br><span class="line">conda install -c bioconda bioconductor-tcgabiolinks=2.22.1 -y</span><br><span class="line">conda install -c bioconda bioconductor-deseq2=1.34.0 -y</span><br><span class="line">conda install -c bioconda bioconductor-rhdf5=2.38.0 -y</span><br><span class="line">conda install -c bioconda bioconductor-limma=3.50.1 -y</span><br><span class="line">conda install -c bioconda bioconductor-apeglm=1.16.0 -y</span><br><span class="line">conda install -c bioconda r-sleuth=0.30.0 -y</span><br><span class="line">conda install -c bioconda r-wasabi=1.0.1 -y</span><br><span class="line">conda install -c conda-forge r-irkernel=1.3 -y</span><br><span class="line">conda install -c conda-forge r-ashr=2.2_54 -y</span><br><span class="line">conda install -c conda-forge r-robustrankaggreg=1.1 -y</span><br><span class="line">conda install -c conda-forge r-devtools=2.4.3 -y</span><br><span class="line">IRkernel::installspec(name=<span class="string">&#x27;tcga&#x27;</span>, displayname=<span class="string">&#x27;r-tcga&#x27;</span>)</span><br></pre></td></tr></table></figure>
<ul>
<li>deseq2 数据要求：低生物学重复 &amp; raw counts；假定负二项分布；适合高通量测序数据</li>
<li>sleuth 数据要求：<strong>Kallisto</strong>输出的结果</li>
<li>limma 数据要求：logCPM；假定正态分布；适合芯片数据</li>
<li><a target="_blank" rel="noopener" href="https://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">fpkm数据差异基因分析</a> ：理论上是不能进行分析的，无计可施时可以参考</li>
<li>高生物学重复请直接使用 <strong>wilcox.test</strong> 以避免大量假阳性</li>
<li>多数据集结果整合：RobustRankAggreg</li>
</ul>
<p>fpkm转tpm示例（基于 SummarizedExperiment 数据框架）</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><span class="line">7</span><br></pre></td><td class="code"><pre><span class="line">fpkmToTpm <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>fpkm<span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">    <span class="built_in">exp</span><span class="punctuation">(</span><span class="built_in">log</span><span class="punctuation">(</span>fpkm<span class="punctuation">)</span> <span class="operator">-</span> <span class="built_in">log</span><span class="punctuation">(</span><span class="built_in">sum</span><span class="punctuation">(</span>fpkm<span class="punctuation">)</span><span class="punctuation">)</span> <span class="operator">+</span> <span class="built_in">log</span><span class="punctuation">(</span><span class="number">1e6</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line">f_fpkmToTpm <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>l_e<span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">     apply<span class="punctuation">(</span>l_e<span class="punctuation">,</span><span class="number">2</span><span class="punctuation">,</span>fpkmToTpm<span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line">assay<span class="punctuation">(</span>sce<span class="punctuation">,</span> <span class="string">&quot;TPM&quot;</span><span class="punctuation">)</span> <span class="operator">&lt;-</span> f_fpkmToTpm<span class="punctuation">(</span>assay<span class="punctuation">(</span>sce<span class="punctuation">,</span> <span class="string">&quot;HTSeq - FPKM&quot;</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
<h2 id="第一步，多组差异基因分析">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><span class="line">library<span class="punctuation">(</span>DESeq2<span class="punctuation">)</span></span><br><span class="line">count_all <span class="operator">&lt;-</span> read.csv<span class="punctuation">(</span><span class="string">&quot;~/upload/zl_liu/star_data/yyz_01/yyz_01.csv&quot;</span><span class="punctuation">,</span>header<span class="operator">=</span><span class="literal">TRUE</span><span class="punctuation">)</span></span><br><span class="line">count_all</span><br><span class="line">cts_b <span class="operator">&lt;-</span> count_all<span class="punctuation">[</span> <span class="punctuation">,</span><span class="built_in">c</span><span class="punctuation">(</span><span class="operator">-</span><span class="number">1</span><span class="punctuation">,</span><span class="operator">-</span><span class="number">2</span><span class="punctuation">,</span><span class="operator">-</span><span class="number">3</span><span class="punctuation">)</span><span class="punctuation">]</span></span><br><span class="line">rownames<span class="punctuation">(</span>cts_b<span class="punctuation">)</span> <span class="operator">&lt;-</span> count_all<span class="operator">$</span>ID</span><br><span class="line">keep <span class="operator">&lt;-</span> rowSums<span class="punctuation">(</span>cts_b<span class="punctuation">)</span> <span class="operator">&gt;</span> ncol<span class="punctuation">(</span>cts_b<span class="punctuation">)</span></span><br><span class="line">cts_b<span class="punctuation">[</span>keep<span class="punctuation">,</span><span class="punctuation">]</span></span><br><span class="line">f_DESeq2 <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>cts_bb<span class="punctuation">,</span> rowInfo<span class="punctuation">,</span> ControlN<span class="punctuation">,</span> TreatN<span class="punctuation">,</span> rm.NA<span class="operator">=</span><span class="built_in">T</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">    cts_b <span class="operator">&lt;-</span> cts_bb<span class="punctuation">[</span><span class="punctuation">,</span><span class="built_in">c</span><span class="punctuation">(</span>ControlN<span class="punctuation">,</span> TreatN<span class="punctuation">)</span><span class="punctuation">]</span></span><br><span class="line">    conditions <span class="operator">&lt;-</span> factor<span class="punctuation">(</span><span class="built_in">c</span><span class="punctuation">(</span><span class="built_in">rep</span><span class="punctuation">(</span><span class="string">&quot;Control&quot;</span><span class="punctuation">,</span><span class="built_in">length</span><span class="punctuation">(</span>ControlN<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">,</span> <span class="built_in">rep</span><span class="punctuation">(</span><span class="string">&quot;Treat&quot;</span><span class="punctuation">,</span><span class="built_in">length</span><span class="punctuation">(</span>TreatN<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">)</span> </span><br><span class="line">    colData_b <span class="operator">&lt;-</span> data.frame<span class="punctuation">(</span>row.names <span class="operator">=</span> colnames<span class="punctuation">(</span>cts_b<span class="punctuation">)</span><span class="punctuation">,</span> conditions<span class="punctuation">)</span></span><br><span class="line">    print<span class="punctuation">(</span>colData_b<span class="punctuation">)</span></span><br><span class="line">    dds <span class="operator">&lt;-</span> DESeqDataSetFromMatrix<span class="punctuation">(</span>countData <span class="operator">=</span> cts_b<span class="punctuation">,</span></span><br><span class="line">                              colData <span class="operator">=</span> colData_b<span class="punctuation">,</span></span><br><span class="line">                              design <span class="operator">=</span> <span class="operator">~</span> conditions<span class="punctuation">)</span></span><br><span class="line">    dds <span class="operator">&lt;-</span> DESeq<span class="punctuation">(</span>dds<span class="punctuation">)</span></span><br><span class="line">    res <span class="operator">&lt;-</span> results<span class="punctuation">(</span>dds<span class="punctuation">)</span></span><br><span class="line">    rres <span class="operator">&lt;-</span> cbind<span class="punctuation">(</span>rowInfo<span class="punctuation">,</span> data.frame<span class="punctuation">(</span>res<span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">    <span class="keyword">if</span><span class="punctuation">(</span>rm.NA<span class="punctuation">)</span><span class="punctuation">&#123;</span>rres <span class="operator">&lt;-</span> rres<span class="punctuation">[</span><span class="operator">!</span><span class="built_in">is.na</span><span class="punctuation">(</span>rres<span class="operator">$</span>padj<span class="punctuation">)</span><span class="punctuation">,</span><span class="punctuation">]</span><span class="punctuation">&#125;</span></span><br><span class="line">    rres <span class="operator">&lt;-</span> rres<span class="punctuation">[</span>order<span class="punctuation">(</span>rres<span class="operator">$</span>log2FoldChange<span class="punctuation">,</span> decreasing <span class="operator">=</span> <span class="built_in">T</span><span class="punctuation">)</span><span class="punctuation">,</span><span class="punctuation">]</span></span><br><span class="line">    saveRDS<span class="punctuation">(</span>rres<span class="punctuation">,</span> paste<span class="punctuation">(</span><span class="string">&#x27;DEGs&#x27;</span><span class="punctuation">,</span> paste<span class="punctuation">(</span>TreatN<span class="punctuation">,</span> collapse <span class="operator">=</span> <span class="string">&#x27;_&#x27;</span><span class="punctuation">)</span><span class="punctuation">,</span> <span class="string">&#x27;vs.&#x27;</span><span class="punctuation">,</span> paste<span class="punctuation">(</span>ControlN<span class="punctuation">,</span> collapse <span class="operator">=</span> <span class="string">&#x27;_&#x27;</span><span class="punctuation">)</span><span class="punctuation">,</span> <span class="string">&#x27;DESeq2.rds&#x27;</span><span class="punctuation">,</span>sep <span class="operator">=</span> <span class="string">&#x27;_&#x27;</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">    rres</span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line">Ct1 <span class="operator">&lt;-</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&#x27;X1.control.DMSO&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;X2.control.DMSO&#x27;</span><span class="punctuation">)</span></span><br><span class="line">Tt1 <span class="operator">&lt;-</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&#x27;X1.OE.DMSO&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;X2.OE.DMSO&#x27;</span><span class="punctuation">)</span></span><br><span class="line">Ct2 <span class="operator">&lt;-</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&#x27;X1.OE.DMSO&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;X2.OE.DMSO&#x27;</span><span class="punctuation">)</span></span><br><span class="line">Tt2 <span class="operator">&lt;-</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&#x27;X1.OE.Enz&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;X2.OE.Enz&#x27;</span><span class="punctuation">)</span></span><br><span class="line">Ct3 <span class="operator">&lt;-</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&#x27;X1.control.Enz&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;X2.control.Enz&#x27;</span><span class="punctuation">)</span></span><br><span class="line">Tt3 <span class="operator">&lt;-</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&#x27;X1.OE.Enz&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;X2.OE.Enz&#x27;</span><span class="punctuation">)</span></span><br><span class="line">Ct4 <span class="operator">&lt;-</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&#x27;X1.CAF.DMSO&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;X2.CAF.DMSO&#x27;</span><span class="punctuation">)</span></span><br><span class="line">Tt4 <span class="operator">&lt;-</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&#x27;X1.CAF.Enz&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;X2.CAF.Enz&#x27;</span><span class="punctuation">)</span></span><br><span class="line">r1 <span class="operator">&lt;-</span> f_DESeq2<span class="punctuation">(</span>cts_b<span class="punctuation">[</span>keep<span class="punctuation">,</span><span class="punctuation">]</span><span class="punctuation">,</span> count_all<span class="punctuation">[</span>keep<span class="punctuation">,</span><span class="built_in">c</span><span class="punctuation">(</span><span class="number">1</span><span class="punctuation">,</span><span class="number">2</span><span class="punctuation">,</span><span class="number">3</span><span class="punctuation">)</span><span class="punctuation">]</span><span class="punctuation">,</span> Ct1<span class="punctuation">,</span> Tt1<span class="punctuation">)</span></span><br><span class="line">r2 <span class="operator">&lt;-</span> f_DESeq2<span class="punctuation">(</span>cts_b<span class="punctuation">[</span>keep<span class="punctuation">,</span><span class="punctuation">]</span><span class="punctuation">,</span> count_all<span class="punctuation">[</span>keep<span class="punctuation">,</span><span class="built_in">c</span><span class="punctuation">(</span><span class="number">1</span><span class="punctuation">,</span><span class="number">2</span><span class="punctuation">,</span><span class="number">3</span><span class="punctuation">)</span><span class="punctuation">]</span><span class="punctuation">,</span> Ct2<span class="punctuation">,</span> Tt2<span class="punctuation">)</span></span><br><span class="line">r3 <span class="operator">&lt;-</span> f_DESeq2<span class="punctuation">(</span>cts_b<span class="punctuation">[</span>keep<span class="punctuation">,</span><span class="punctuation">]</span><span class="punctuation">,</span> count_all<span class="punctuation">[</span>keep<span class="punctuation">,</span><span class="built_in">c</span><span class="punctuation">(</span><span class="number">1</span><span class="punctuation">,</span><span class="number">2</span><span class="punctuation">,</span><span class="number">3</span><span class="punctuation">)</span><span class="punctuation">]</span><span class="punctuation">,</span> Ct3<span class="punctuation">,</span> Tt3<span class="punctuation">)</span></span><br><span class="line">r4 <span class="operator">&lt;-</span> f_DESeq2<span class="punctuation">(</span>cts_b<span class="punctuation">[</span>keep<span class="punctuation">,</span><span class="punctuation">]</span><span class="punctuation">,</span> count_all<span class="punctuation">[</span>keep<span class="punctuation">,</span><span class="built_in">c</span><span class="punctuation">(</span><span class="number">1</span><span class="punctuation">,</span><span class="number">2</span><span class="punctuation">,</span><span class="number">3</span><span class="punctuation">)</span><span class="punctuation">]</span><span class="punctuation">,</span> Ct4<span class="punctuation">,</span> Tt4<span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
<h2 id="第二步，RRA聚合差异结果">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><span class="line">require<span class="punctuation">(</span>RobustRankAggreg<span class="punctuation">)</span></span><br><span class="line">f_dflist_RRA <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>dflist<span class="punctuation">,</span> nameN<span class="punctuation">,</span> N<span class="punctuation">,</span> orderN<span class="punctuation">,</span> decreasing<span class="operator">=</span><span class="built_in">T</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">    res <span class="operator">&lt;-</span> <span class="built_in">list</span><span class="punctuation">(</span><span class="punctuation">)</span></span><br><span class="line">    <span class="keyword">for</span> <span class="punctuation">(</span>name <span class="keyword">in</span> <span class="built_in">names</span><span class="punctuation">(</span>dflist<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">        tmp <span class="operator">&lt;-</span> dflist<span class="punctuation">[[</span>name<span class="punctuation">]</span><span class="punctuation">]</span></span><br><span class="line">        <span class="keyword">if</span> <span class="punctuation">(</span>nrow<span class="punctuation">(</span>tmp<span class="punctuation">)</span> <span class="operator">==</span> <span class="number">1</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">            res<span class="punctuation">[[</span>name<span class="punctuation">]</span><span class="punctuation">]</span> <span class="operator">&lt;-</span> tmp<span class="punctuation">[</span><span class="number">1</span><span class="punctuation">,</span> nameN<span class="punctuation">]</span></span><br><span class="line">        <span class="punctuation">&#125;</span><span class="keyword">else</span> <span class="keyword">if</span><span class="punctuation">(</span>nrow<span class="punctuation">(</span>tmp<span class="punctuation">)</span> <span class="operator">&gt;=</span><span class="number">2</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">            res<span class="punctuation">[[</span>name<span class="punctuation">]</span><span class="punctuation">]</span> <span class="operator">&lt;-</span> tmp<span class="punctuation">[</span>order<span class="punctuation">(</span>tmp<span class="punctuation">[[</span>orderN<span class="punctuation">]</span><span class="punctuation">]</span><span class="punctuation">,</span>decreasing <span class="operator">=</span> decreasing<span class="punctuation">)</span><span class="punctuation">,</span> nameN<span class="punctuation">]</span></span><br><span class="line">        <span class="punctuation">&#125;</span></span><br><span class="line">    <span class="punctuation">&#125;</span></span><br><span class="line">    <span class="keyword">if</span><span class="punctuation">(</span><span class="built_in">length</span><span class="punctuation">(</span>res<span class="punctuation">)</span> <span class="operator">&lt;</span> <span class="number">1</span><span class="punctuation">)</span><span class="punctuation">&#123;</span> <span class="built_in">return</span><span class="punctuation">(</span><span class="literal">NULL</span><span class="punctuation">)</span><span class="punctuation">&#125;</span></span><br><span class="line">    aggregateRanks<span class="punctuation">(</span>glist <span class="operator">=</span> res<span class="punctuation">,</span> N <span class="operator">=</span> N<span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line">rownames<span class="punctuation">(</span>count_all<span class="punctuation">)</span> <span class="operator">&lt;-</span> count_all<span class="operator">$</span>ID</span><br><span class="line"> </span><br><span class="line">r <span class="operator">&lt;-</span> <span class="built_in">list</span><span class="punctuation">(</span>r1<span class="operator">=</span>r1<span class="punctuation">,</span>r2<span class="operator">=</span>r2<span class="punctuation">,</span>r3<span class="operator">=</span>r3<span class="punctuation">,</span>r4<span class="operator">=</span>r4<span class="punctuation">)</span></span><br><span class="line">r <span class="operator">&lt;-</span> lapply<span class="punctuation">(</span>r<span class="punctuation">,</span> FUN <span class="operator">=</span> <span class="keyword">function</span><span class="punctuation">(</span>x<span class="punctuation">)</span><span class="punctuation">&#123;</span>subset<span class="punctuation">(</span>x<span class="punctuation">,</span> padj<span class="operator">&lt;</span><span class="number">0.05</span> <span class="operator">&amp;</span> log2FoldChange <span class="operator">&gt;</span> <span class="number">1</span><span class="punctuation">)</span><span class="punctuation">&#125;</span><span class="punctuation">)</span></span><br><span class="line">r <span class="operator">&lt;-</span> f_dflist_RRA<span class="punctuation">(</span>r<span class="punctuation">,</span> <span class="string">&#x27;ID&#x27;</span><span class="punctuation">,</span> <span class="built_in">sum</span><span class="punctuation">(</span>keep<span class="punctuation">)</span><span class="punctuation">,</span> <span class="string">&#x27;log2FoldChange&#x27;</span><span class="punctuation">)</span></span><br><span class="line">r <span class="operator">&lt;-</span> cbind<span class="punctuation">(</span>count_all<span class="punctuation">[</span>r<span class="operator">$</span>Name<span class="punctuation">,</span><span class="built_in">c</span><span class="punctuation">(</span><span class="number">2</span><span class="punctuation">,</span><span class="number">3</span><span class="punctuation">)</span><span class="punctuation">]</span><span class="punctuation">,</span> r<span class="punctuation">)</span></span><br><span class="line">r</span><br><span class="line">write.csv<span class="punctuation">(</span>r<span class="punctuation">,</span> <span class="string">&#x27;RRA_up.csv&#x27;</span><span class="punctuation">)</span></span><br><span class="line"> </span><br><span class="line">r <span class="operator">&lt;-</span> <span class="built_in">list</span><span class="punctuation">(</span>r1<span class="operator">=</span>r1<span class="punctuation">,</span>r2<span class="operator">=</span>r2<span class="punctuation">,</span>r3<span class="operator">=</span>r3<span class="punctuation">,</span>r4<span class="operator">=</span>r4<span class="punctuation">)</span></span><br><span class="line">r <span class="operator">&lt;-</span> lapply<span class="punctuation">(</span>r<span class="punctuation">,</span> FUN <span class="operator">=</span> <span class="keyword">function</span><span class="punctuation">(</span>x<span class="punctuation">)</span><span class="punctuation">&#123;</span>subset<span class="punctuation">(</span>x<span class="punctuation">,</span> padj<span class="operator">&lt;</span><span class="number">0.05</span> <span class="operator">&amp;</span> log2FoldChange <span class="operator">&lt;</span> <span class="operator">-</span><span class="number">1</span><span class="punctuation">)</span><span class="punctuation">&#125;</span><span class="punctuation">)</span></span><br><span class="line">r <span class="operator">&lt;-</span> f_dflist_RRA<span class="punctuation">(</span>r<span class="punctuation">,</span> <span class="string">&#x27;ID&#x27;</span><span class="punctuation">,</span> <span class="built_in">sum</span><span class="punctuation">(</span>keep<span class="punctuation">)</span><span class="punctuation">,</span> <span class="string">&#x27;log2FoldChange&#x27;</span><span class="punctuation">,</span> decreasing <span class="operator">=</span> <span class="built_in">F</span><span class="punctuation">)</span></span><br><span class="line">r <span class="operator">&lt;-</span> cbind<span class="punctuation">(</span>count_all<span class="punctuation">[</span>r<span class="operator">$</span>Name<span class="punctuation">,</span><span class="built_in">c</span><span class="punctuation">(</span><span class="number">2</span><span class="punctuation">,</span><span class="number">3</span><span class="punctuation">)</span><span class="punctuation">]</span><span class="punctuation">,</span> r<span class="punctuation">)</span></span><br><span class="line">r</span><br><span class="line">write.csv<span class="punctuation">(</span>r<span class="punctuation">,</span> <span class="string">&#x27;RRA_down.csv&#x27;</span><span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
<h2 id="附加：绘图">附加：绘图</h2>
<h3 id="安装包">安装包</h3>
<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><span class="line">9</span><br></pre></td><td class="code"><pre><span class="line">conda create -n rsf -c conda-forge r-sf=1.0_4</span><br><span class="line">conda activate rsf</span><br><span class="line">library(sf)</span><br><span class="line"><span class="comment"># install.packages(&quot;sf&quot;, version = &quot;1.0-4&quot;)</span></span><br><span class="line">install.packages(<span class="string">&quot;ggVennDiagram&quot;</span>)</span><br><span class="line">conda install -c conda-forge r-ggsci -y</span><br><span class="line">conda install -c conda-forge r-irkernel -y</span><br><span class="line">Rscript -e <span class="string">&quot;IRkernel::installspec(name=&#x27;ggVennDiagram&#x27;, displayname=&#x27;r-ggVennDiagram&#x27;)&quot;</span></span><br><span class="line">conda install -c conda-forge r-venndiagram -y</span><br></pre></td></tr></table></figure>
<h3 id="数据准备">数据准备</h3>
<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><span class="line">x <span class="operator">&lt;-</span> <span class="built_in">list</span><span class="punctuation">(</span><span class="punctuation">)</span></span><br><span class="line">r <span class="operator">&lt;-</span> <span class="built_in">list</span><span class="punctuation">(</span><span class="punctuation">)</span></span><br><span class="line">r<span class="operator">$</span>cell <span class="operator">&lt;-</span> readRDS<span class="punctuation">(</span><span class="string">&#x27;../A_ref_A_fiig.1_A/DEG.rds&#x27;</span><span class="punctuation">)</span></span><br><span class="line">r<span class="operator">$</span>tissue <span class="operator">&lt;-</span> readRDS<span class="punctuation">(</span><span class="string">&#x27;../B_ref_A_fiig.1_A/DEG.rds&#x27;</span><span class="punctuation">)</span></span><br><span class="line"><span class="built_in">names</span><span class="punctuation">(</span>r<span class="operator">$</span>tissue<span class="punctuation">)</span><span class="punctuation">[</span><span class="number">3</span><span class="punctuation">]</span> <span class="operator">&lt;-</span> <span class="string">&#x27;symbol&#x27;</span></span><br><span class="line">r_up <span class="operator">&lt;-</span> lapply<span class="punctuation">(</span>r<span class="punctuation">,</span> FUN <span class="operator">=</span> <span class="keyword">function</span><span class="punctuation">(</span>x<span class="punctuation">)</span><span class="punctuation">&#123;</span>subset<span class="punctuation">(</span>x<span class="punctuation">,</span> log2FoldChange <span class="operator">&gt;</span> <span class="number">0</span><span class="punctuation">)</span><span class="punctuation">&#125;</span><span class="punctuation">)</span></span><br><span class="line">x<span class="operator">$</span>cell_up <span class="operator">&lt;-</span> r_up<span class="operator">$</span>cell<span class="operator">$</span>symbol</span><br><span class="line">x<span class="operator">$</span>RRA_up <span class="operator">&lt;-</span> readRDS<span class="punctuation">(</span><span class="string">&#x27;r_up.rds&#x27;</span><span class="punctuation">)</span></span><br><span class="line">x<span class="operator">$</span>RRA_up <span class="operator">&lt;-</span> x<span class="operator">$</span>RRA_up<span class="operator">$</span>Name</span><br><span class="line">x<span class="operator">$</span>tissue_up <span class="operator">&lt;-</span> r_up<span class="operator">$</span>tissue<span class="operator">$</span>symbol</span><br><span class="line">r_dn <span class="operator">&lt;-</span> lapply<span class="punctuation">(</span>r<span class="punctuation">,</span> FUN <span class="operator">=</span> <span class="keyword">function</span><span class="punctuation">(</span>x<span class="punctuation">)</span><span class="punctuation">&#123;</span>subset<span class="punctuation">(</span>x<span class="punctuation">,</span> log2FoldChange <span class="operator">&lt;</span> <span class="number">0</span><span class="punctuation">)</span><span class="punctuation">&#125;</span><span class="punctuation">)</span></span><br><span class="line">x<span class="operator">$</span>cell_down <span class="operator">&lt;-</span> r_dn<span class="operator">$</span>cell<span class="operator">$</span>symbol</span><br><span class="line">x<span class="operator">$</span>RRA_down <span class="operator">&lt;-</span> readRDS<span class="punctuation">(</span><span class="string">&#x27;r_dn.rds&#x27;</span><span class="punctuation">)</span></span><br><span class="line">x<span class="operator">$</span>RRA_down <span class="operator">&lt;-</span> x<span class="operator">$</span>RRA_down<span class="operator">$</span>Name</span><br><span class="line">x<span class="operator">$</span>tissue_down <span class="operator">&lt;-</span> r_dn<span class="operator">$</span>tissue<span class="operator">$</span>symbol</span><br><span class="line">summary<span class="punctuation">(</span>x<span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
<h3 id="绘图1">绘图1</h3>
<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></pre></td><td class="code"><pre><span class="line"><span class="comment">#载入所需的R包；</span></span><br><span class="line">library<span class="punctuation">(</span>ggplot2<span class="punctuation">)</span></span><br><span class="line">library<span class="punctuation">(</span>ggsci<span class="punctuation">)</span></span><br><span class="line">library<span class="punctuation">(</span>sf<span class="punctuation">)</span></span><br><span class="line">library<span class="punctuation">(</span>ggVennDiagram<span class="punctuation">)</span></span><br><span class="line">color4 <span class="operator">&lt;-</span> alpha<span class="punctuation">(</span><span class="string">&quot;#99CC00&quot;</span><span class="punctuation">,</span><span class="number">0.5</span><span class="punctuation">)</span></span><br><span class="line">ggVennDiagram<span class="punctuation">(</span>x<span class="punctuation">[</span><span class="number">1</span><span class="operator">:</span><span class="number">6</span><span class="punctuation">]</span><span class="punctuation">,</span> label_alpha<span class="operator">=</span><span class="number">0</span><span class="punctuation">)</span> <span class="operator">+</span></span><br><span class="line">  scale_fill_gradient<span class="punctuation">(</span>low<span class="operator">=</span><span class="string">&#x27;white&#x27;</span><span class="punctuation">,</span>high <span class="operator">=</span>color4<span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
<h3 id="绘图2">绘图2</h3>
<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></pre></td><td class="code"><pre><span class="line">venn.plot <span class="operator">&lt;-</span> venn.diagram<span class="punctuation">(</span></span><br><span class="line">    x <span class="operator">=</span> x<span class="punctuation">[</span><span class="number">1</span><span class="operator">:</span><span class="number">3</span><span class="punctuation">]</span><span class="punctuation">,</span></span><br><span class="line">    filename <span class="operator">=</span> <span class="literal">NULL</span><span class="punctuation">,</span></span><br><span class="line">    cex <span class="operator">=</span> <span class="number">2.5</span><span class="punctuation">,</span></span><br><span class="line">    cat.cex <span class="operator">=</span> <span class="number">2.5</span><span class="punctuation">,</span></span><br><span class="line">    cat.dist <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="number">0.07</span><span class="punctuation">,</span> <span class="number">0.07</span><span class="punctuation">,</span> <span class="number">0.02</span><span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">    cat.pos <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="operator">-</span><span class="number">20</span><span class="punctuation">,</span> <span class="number">20</span><span class="punctuation">,</span> <span class="number">20</span><span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">    alpha <span class="operator">=</span> <span class="number">0.5</span><span class="punctuation">,</span></span><br><span class="line">    fill <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&quot;#99CC00&quot;</span><span class="punctuation">,</span> <span class="string">&quot;#c77cff&quot;</span><span class="punctuation">,</span> <span class="string">&#x27;#f8766d&#x27;</span><span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">)</span>;</span><br><span class="line">grid.draw<span class="punctuation">(</span>venn.plot<span class="punctuation">)</span></span><br><span class="line">venn.plot <span class="operator">&lt;-</span> venn.diagram<span class="punctuation">(</span></span><br><span class="line">    x <span class="operator">=</span> x<span class="punctuation">[</span><span class="number">4</span><span class="operator">:</span><span class="number">6</span><span class="punctuation">]</span><span class="punctuation">,</span></span><br><span class="line">    filename <span class="operator">=</span> <span class="literal">NULL</span><span class="punctuation">,</span></span><br><span class="line">    cex <span class="operator">=</span> <span class="number">2.5</span><span class="punctuation">,</span></span><br><span class="line">    cat.cex <span class="operator">=</span> <span class="number">2.5</span><span class="punctuation">,</span></span><br><span class="line">    cat.dist <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="number">0.07</span><span class="punctuation">,</span> <span class="number">0.07</span><span class="punctuation">,</span> <span class="number">0.02</span><span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">    cat.pos <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="operator">-</span><span class="number">20</span><span class="punctuation">,</span> <span class="number">20</span><span class="punctuation">,</span> <span class="number">20</span><span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">    alpha <span class="operator">=</span> <span class="number">0.5</span><span class="punctuation">,</span></span><br><span class="line">    fill <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&quot;#99CC00&quot;</span><span class="punctuation">,</span> <span class="string">&quot;#c77cff&quot;</span><span class="punctuation">,</span> <span class="string">&#x27;#f8766d&#x27;</span><span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">)</span>;</span><br><span class="line">grid.draw<span class="punctuation">(</span>venn.plot<span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
<h2 id="附加：单细胞数据">附加：单细胞数据</h2>
<h3 id="第一步-读取数据">第一步 读取数据</h3>
<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><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br><span class="line">39</span><br><span class="line">40</span><br><span class="line">41</span><br><span class="line">42</span><br><span class="line">43</span><br><span class="line">44</span><br><span class="line">45</span><br></pre></td><td class="code"><pre><span class="line">library<span class="punctuation">(</span>Seurat<span class="punctuation">)</span></span><br><span class="line">library<span class="punctuation">(</span>plyr<span class="punctuation">)</span></span><br><span class="line">library<span class="punctuation">(</span>dplyr<span class="punctuation">)</span></span><br><span class="line">library<span class="punctuation">(</span>patchwork<span class="punctuation">)</span></span><br><span class="line">library<span class="punctuation">(</span>purrr<span class="punctuation">)</span></span><br><span class="line">f_metadata_removeNA <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>sObject<span class="punctuation">,</span> lc_groupN<span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">    sObject<span class="operator">@</span>meta.data <span class="operator">&lt;-</span> sObject<span class="operator">@</span>meta.data<span class="punctuation">[</span>colnames<span class="punctuation">(</span>sObject<span class="punctuation">)</span><span class="punctuation">,</span><span class="punctuation">]</span></span><br><span class="line">    sObject <span class="operator">&lt;-</span> subset<span class="punctuation">(</span>x <span class="operator">=</span> sObject<span class="punctuation">,</span> <span class="operator">!</span><span class="operator">!</span>sym<span class="punctuation">(</span>lc_groupN<span class="punctuation">)</span><span class="operator">%in%</span>f_br_cluster_f<span class="punctuation">(</span>sObject<span class="punctuation">,</span> lc_groupN<span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">    sObject</span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line">f_br_cluster_f <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>sObject<span class="punctuation">,</span> lc_groupN<span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">    lc_filter <span class="operator">&lt;-</span> unlist<span class="punctuation">(</span>unique<span class="punctuation">(</span>sObject<span class="punctuation">[[</span>lc_groupN<span class="punctuation">]</span><span class="punctuation">]</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">    lc_filter <span class="operator">&lt;-</span> lc_filter<span class="punctuation">[</span><span class="operator">!</span><span class="built_in">is.na</span><span class="punctuation">(</span>lc_filter<span class="punctuation">)</span><span class="punctuation">]</span></span><br><span class="line">    lc_filter</span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line"></span><br><span class="line">scRNA_split <span class="operator">=</span> readRDS<span class="punctuation">(</span><span class="string">&quot;~/zlliu/R_output/21.09.21.SingleR/scRNA.rds&quot;</span><span class="punctuation">)</span></span><br><span class="line">scRNA_split <span class="operator">&lt;-</span> f_metadata_removeNA<span class="punctuation">(</span>scRNA_split<span class="punctuation">,</span> <span class="string">&#x27;Region&#x27;</span><span class="punctuation">)</span></span><br><span class="line"></span><br><span class="line">n_ExN <span class="operator">&lt;-</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&#x27;L4 IT&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;L5 IT&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;L5 ET&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;IT&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;L6b&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;L5/6 IT Car3&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;L6 IT&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;L2/3 IT&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;L5/6 NP&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;L6 IT Car3&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;L6 CT&#x27;</span><span class="punctuation">)</span></span><br><span class="line">n_InN <span class="operator">&lt;-</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&#x27;Lamp5&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;Pvalb&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;Sst&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;Vip&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;Sncg&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;PAX6&#x27;</span><span class="punctuation">)</span></span><br><span class="line">n_NoN <span class="operator">&lt;-</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&#x27;Astro&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;Endo&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;Micro-PVM&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;OPC&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;Oligo&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;Pericyte&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;VLMC&#x27;</span><span class="punctuation">)</span></span><br><span class="line">n_groups <span class="operator">&lt;-</span> <span class="built_in">list</span><span class="punctuation">(</span>NoN<span class="operator">=</span>n_NoN<span class="punctuation">,</span> ExN<span class="operator">=</span>n_ExN<span class="punctuation">,</span> InN<span class="operator">=</span>n_InN<span class="punctuation">)</span></span><br><span class="line"></span><br><span class="line">f_listUpdateRe <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>lc_obj<span class="punctuation">,</span> lc_bool<span class="punctuation">,</span> lc_item<span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">    lc_obj<span class="punctuation">[</span>lc_bool<span class="punctuation">]</span> <span class="operator">&lt;-</span> <span class="built_in">rep</span><span class="punctuation">(</span>lc_item<span class="punctuation">,</span>times<span class="operator">=</span><span class="built_in">sum</span><span class="punctuation">(</span>lc_bool<span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">    lc_obj</span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line">f_grouplabel <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>lc_meta.data<span class="punctuation">,</span> lc_groups<span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">    res <span class="operator">&lt;-</span> lc_meta.data<span class="punctuation">[[</span><span class="number">1</span><span class="punctuation">]</span><span class="punctuation">]</span></span><br><span class="line">    <span class="keyword">for</span><span class="punctuation">(</span>lc_g <span class="keyword">in</span> <span class="built_in">names</span><span class="punctuation">(</span>lc_groups<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">        lc_bool <span class="operator">=</span> <span class="punctuation">(</span>res <span class="operator">%in%</span> lc_groups<span class="punctuation">[[</span>lc_g<span class="punctuation">]</span><span class="punctuation">]</span><span class="punctuation">)</span></span><br><span class="line">        <span class="keyword">for</span><span class="punctuation">(</span>c_n <span class="keyword">in</span> colnames<span class="punctuation">(</span>lc_meta.data<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">            lc_bool <span class="operator">=</span> lc_bool  <span class="punctuation">(</span>lc_meta.data<span class="punctuation">[[</span>c_n<span class="punctuation">]</span><span class="punctuation">]</span> <span class="operator">%in%</span> lc_groups<span class="punctuation">[[</span>lc_g<span class="punctuation">]</span><span class="punctuation">]</span><span class="punctuation">)</span></span><br><span class="line">        <span class="punctuation">&#125;</span></span><br><span class="line">        res <span class="operator">&lt;-</span> f_listUpdateRe<span class="punctuation">(</span>res<span class="punctuation">,</span> lc_bool<span class="punctuation">,</span> lc_g<span class="punctuation">)</span></span><br><span class="line">    <span class="punctuation">&#125;</span></span><br><span class="line">    <span class="built_in">names</span><span class="punctuation">(</span>res<span class="punctuation">)</span> <span class="operator">&lt;-</span> rownames<span class="punctuation">(</span>lc_meta.data<span class="punctuation">)</span></span><br><span class="line">    res</span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line"></span><br><span class="line">scRNA_split<span class="punctuation">[[</span><span class="string">&#x27;n_groups&#x27;</span><span class="punctuation">]</span><span class="punctuation">]</span> <span class="operator">&lt;-</span> f_grouplabel<span class="punctuation">(</span>scRNA_split<span class="punctuation">[[</span><span class="built_in">c</span><span class="punctuation">(</span><span class="string">&quot;hM1_hmca_class&quot;</span><span class="punctuation">)</span><span class="punctuation">]</span><span class="punctuation">]</span><span class="punctuation">,</span> n_groups<span class="punctuation">)</span></span><br><span class="line">sc_Neuron <span class="operator">&lt;-</span> subset<span class="punctuation">(</span>x <span class="operator">=</span> scRNA_split<span class="punctuation">,</span> n_groups <span class="operator">%in%</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&quot;InN&quot;</span><span class="punctuation">,</span> <span class="string">&quot;ExN&quot;</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line"></span><br><span class="line">samples <span class="operator">&lt;-</span> SplitObject<span class="punctuation">(</span>object <span class="operator">=</span> sc_Neuron<span class="punctuation">,</span> split.by <span class="operator">=</span> <span class="string">&#x27;orig.ident&#x27;</span><span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
<h3 id="第二步-计算差异基因">第二步 计算差异基因</h3>
<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><span class="line">DEGs <span class="operator">&lt;-</span> <span class="built_in">list</span><span class="punctuation">(</span><span class="punctuation">)</span></span><br><span class="line"><span class="keyword">for</span> <span class="punctuation">(</span>name <span class="keyword">in</span> <span class="built_in">names</span><span class="punctuation">(</span>samples<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">    tmp <span class="operator">&lt;-</span> samples<span class="punctuation">[[</span>name<span class="punctuation">]</span><span class="punctuation">]</span></span><br><span class="line">    Idents<span class="punctuation">(</span>tmp<span class="punctuation">)</span> <span class="operator">&lt;-</span> <span class="string">&#x27;Region&#x27;</span></span><br><span class="line">    DEGs<span class="punctuation">[[</span>name<span class="punctuation">]</span><span class="punctuation">]</span> <span class="operator">=</span> FindAllMarkers<span class="punctuation">(</span>tmp<span class="punctuation">,</span> only.pos <span class="operator">=</span> <span class="built_in">T</span><span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">&#125;</span></span><br></pre></td></tr></table></figure>
<h3 id="第三步-整合数据">第三步 整合数据</h3>
<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></pre></td><td class="code"><pre><span class="line">f_dflist_subset <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>dflist<span class="punctuation">,</span> nameN<span class="operator">=</span><span class="literal">NULL</span><span class="punctuation">,</span> ...<span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">    res <span class="operator">&lt;-</span> <span class="built_in">list</span><span class="punctuation">(</span><span class="punctuation">)</span></span><br><span class="line">    <span class="keyword">for</span> <span class="punctuation">(</span>name <span class="keyword">in</span> <span class="built_in">names</span><span class="punctuation">(</span>dflist<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">        res<span class="punctuation">[[</span>name<span class="punctuation">]</span><span class="punctuation">]</span> <span class="operator">&lt;-</span> subset<span class="punctuation">(</span>dflist<span class="punctuation">[[</span>name<span class="punctuation">]</span><span class="punctuation">]</span><span class="punctuation">,</span> ...<span class="punctuation">)</span></span><br><span class="line">    <span class="punctuation">&#125;</span></span><br><span class="line">    res</span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line">require<span class="punctuation">(</span>RobustRankAggreg<span class="punctuation">)</span></span><br><span class="line">f_dflist_RRA <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>dflist<span class="punctuation">,</span> nameN<span class="punctuation">,</span> N<span class="punctuation">,</span> orderN<span class="punctuation">,</span> decreasing<span class="operator">=</span><span class="built_in">T</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">    res <span class="operator">&lt;-</span> <span class="built_in">list</span><span class="punctuation">(</span><span class="punctuation">)</span></span><br><span class="line">    <span class="keyword">for</span> <span class="punctuation">(</span>name <span class="keyword">in</span> <span class="built_in">names</span><span class="punctuation">(</span>dflist<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">        tmp <span class="operator">&lt;-</span> dflist<span class="punctuation">[[</span>name<span class="punctuation">]</span><span class="punctuation">]</span></span><br><span class="line">        <span class="keyword">if</span> <span class="punctuation">(</span>nrow<span class="punctuation">(</span>tmp<span class="punctuation">)</span> <span class="operator">==</span> <span class="number">1</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">            res<span class="punctuation">[[</span>name<span class="punctuation">]</span><span class="punctuation">]</span> <span class="operator">&lt;-</span> tmp<span class="punctuation">[</span><span class="number">1</span><span class="punctuation">,</span> nameN<span class="punctuation">]</span></span><br><span class="line">        <span class="punctuation">&#125;</span><span class="keyword">else</span> <span class="keyword">if</span><span class="punctuation">(</span>nrow<span class="punctuation">(</span>tmp<span class="punctuation">)</span> <span class="operator">&gt;=</span><span class="number">2</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">            res<span class="punctuation">[[</span>name<span class="punctuation">]</span><span class="punctuation">]</span> <span class="operator">&lt;-</span> tmp<span class="punctuation">[</span>order<span class="punctuation">(</span>tmp<span class="punctuation">[[</span>orderN<span class="punctuation">]</span><span class="punctuation">]</span><span class="punctuation">,</span>decreasing <span class="operator">=</span> decreasing<span class="punctuation">)</span><span class="punctuation">,</span> nameN<span class="punctuation">]</span></span><br><span class="line">        <span class="punctuation">&#125;</span></span><br><span class="line">    <span class="punctuation">&#125;</span></span><br><span class="line">    <span class="keyword">if</span><span class="punctuation">(</span><span class="built_in">length</span><span class="punctuation">(</span>res<span class="punctuation">)</span> <span class="operator">&lt;</span> <span class="number">1</span><span class="punctuation">)</span><span class="punctuation">&#123;</span> <span class="built_in">return</span><span class="punctuation">(</span><span class="literal">NULL</span><span class="punctuation">)</span><span class="punctuation">&#125;</span></span><br><span class="line">    aggregateRanks<span class="punctuation">(</span>glist <span class="operator">=</span> res<span class="punctuation">,</span> N <span class="operator">=</span> N<span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">&#125;</span></span><br></pre></td></tr></table></figure>
<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></pre></td><td class="code"><pre><span class="line">res <span class="operator">&lt;-</span> data.frame<span class="punctuation">(</span><span class="punctuation">)</span></span><br><span class="line"><span class="keyword">for</span><span class="punctuation">(</span>name <span class="keyword">in</span> unique<span class="punctuation">(</span>sc_Neuron<span class="operator">@</span>meta.data<span class="operator">$</span>Region<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">    tmp <span class="operator">&lt;-</span> f_dflist_subset<span class="punctuation">(</span>DEGs<span class="punctuation">,</span> name<span class="punctuation">,</span> cluster<span class="operator">==</span>nameN<span class="punctuation">)</span></span><br><span class="line">    tmp <span class="operator">&lt;-</span> f_dflist_RRA<span class="punctuation">(</span>tmp<span class="punctuation">,</span> <span class="string">&#x27;gene&#x27;</span><span class="punctuation">,</span> N<span class="operator">=</span><span class="number">24223</span><span class="punctuation">,</span> <span class="string">&#x27;avg_log2FC&#x27;</span><span class="punctuation">,</span> decreasing <span class="operator">=</span> <span class="built_in">T</span><span class="punctuation">)</span></span><br><span class="line">    <span class="keyword">if</span><span class="punctuation">(</span><span class="operator">!</span><span class="built_in">is.null</span><span class="punctuation">(</span>tmp<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">        tmp<span class="punctuation">[[</span><span class="string">&#x27;cluster&#x27;</span><span class="punctuation">]</span><span class="punctuation">]</span> <span class="operator">&lt;-</span> name</span><br><span class="line">        res <span class="operator">&lt;-</span> rbind<span class="punctuation">(</span>res<span class="punctuation">,</span> tmp<span class="punctuation">)</span></span><br><span class="line">    <span class="punctuation">&#125;</span></span><br><span class="line"><span class="punctuation">&#125;</span></span><br></pre></td></tr></table></figure>
<h3 id="第四步-保存结果">第四步 保存结果</h3>
<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></pre></td><td class="code"><pre><span class="line">require<span class="punctuation">(</span>openxlsx<span class="punctuation">)</span></span><br><span class="line">wb <span class="operator">&lt;-</span> createWorkbook<span class="punctuation">(</span><span class="punctuation">)</span></span><br><span class="line"><span class="keyword">for</span> <span class="punctuation">(</span>name <span class="keyword">in</span> <span class="built_in">names</span><span class="punctuation">(</span>samples<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">    addWorksheet<span class="punctuation">(</span>wb <span class="operator">=</span> wb<span class="punctuation">,</span> sheetName <span class="operator">=</span> name<span class="punctuation">)</span></span><br><span class="line">    writeData<span class="punctuation">(</span>wb <span class="operator">=</span> wb<span class="punctuation">,</span> sheet <span class="operator">=</span> name<span class="punctuation">,</span> x <span class="operator">=</span> DEGs<span class="punctuation">[[</span>name<span class="punctuation">]</span><span class="punctuation">]</span><span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line">addWorksheet<span class="punctuation">(</span>wb <span class="operator">=</span> wb<span class="punctuation">,</span> sheetName <span class="operator">=</span> <span class="string">&#x27;RRA&#x27;</span><span class="punctuation">)</span></span><br><span class="line">writeData<span class="punctuation">(</span>wb <span class="operator">=</span> wb<span class="punctuation">,</span> sheet <span class="operator">=</span> <span class="string">&#x27;RRA&#x27;</span><span class="punctuation">,</span> x <span class="operator">=</span> res<span class="punctuation">)</span></span><br><span class="line">saveWorkbook<span class="punctuation">(</span>wb<span class="punctuation">,</span> <span class="string">&quot;DEG_Brain_Regin_Neuron.xlsx&quot;</span><span class="punctuation">,</span> overwrite <span class="operator">=</span> <span class="literal">TRUE</span><span class="punctuation">)</span></span><br></pre></td></tr></table></figure>

                
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