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            <h1 id="seo-header">TCGAbiolinks下载甲基化数据（续）</h1>
            
            
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                <p>之前<a target="_blank" rel="noopener" href="https://occdn.limour.top/2310.html">TCGAbiolinks下载甲基化数据</a>的hg19的数据下载好了，现在继续进行分析</p>
<h2 id="安装包"><a href="#安装包" class="headerlink" title="安装包"></a>安装包</h2><ul>
<li>conda create -n rGADEM -c conda-forge r-base&#x3D;3.6 -y</li>
<li>conda activate rGADEM</li>
<li>conda install -c bioconda bioconductor-motiv -y</li>
<li>conda install -c conda-forge libopenblas -y</li>
<li>conda install -c conda-forge openblas -y</li>
<li>install.packages(‘Matrix’)</li>
<li>conda install -c conda-forge r-irkernel -y</li>
<li>Rscript -e “IRkernel::installspec(name&#x3D;’rGADEM’, displayname&#x3D;’r-rGADEM’)”</li>
</ul>
<h2 id="定义函数"><a href="#定义函数" class="headerlink" title="定义函数"></a>定义函数</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br></pre></td><td class="code"><pre><code class="hljs R">require<span class="hljs-punctuation">(</span>rGADEM<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>GenomicRanges<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>motifStack<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>dplyr<span class="hljs-punctuation">)</span><br>f_gadem <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>probes<span class="hljs-punctuation">,</span> seqname<span class="hljs-punctuation">,</span> delta_start <span class="hljs-operator">=</span> <span class="hljs-number">100</span><span class="hljs-punctuation">,</span> delta_end <span class="hljs-operator">=</span> <span class="hljs-number">100</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    probes_tmp <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>probes<span class="hljs-punctuation">,</span> seqnames<span class="hljs-operator">==</span>seqname<span class="hljs-punctuation">)</span><br>    sequence <span class="hljs-operator">&lt;-</span> GRanges<span class="hljs-punctuation">(</span><br>      seqnames <span class="hljs-operator">=</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span>seqname<span class="hljs-punctuation">,</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>probes_tmp<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>      IRanges<span class="hljs-punctuation">(</span><br>        start <span class="hljs-operator">=</span> ranges<span class="hljs-punctuation">(</span>probes_tmp<span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> as.data.frame<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> dplyr<span class="hljs-operator">::</span>pull<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;start&quot;</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">-</span> <span class="hljs-number">100</span><span class="hljs-punctuation">,</span><br>        end <span class="hljs-operator">=</span> ranges<span class="hljs-punctuation">(</span>probes_tmp<span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> as.data.frame<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> dplyr<span class="hljs-operator">::</span>pull<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;end&quot;</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> <span class="hljs-number">100</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <br>      strand <span class="hljs-operator">=</span> <span class="hljs-string">&quot;*&quot;</span><br>    <span class="hljs-punctuation">)</span><br>    gadem <span class="hljs-operator">&lt;-</span> GADEM<span class="hljs-punctuation">(</span>sequence<span class="hljs-punctuation">,</span> verbose <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span> genome <span class="hljs-operator">=</span> BSgenome.Hsapiens.UCSC.hg19<span class="hljs-operator">::</span>Hsapiens<span class="hljs-punctuation">)</span><br>    gadem<br><span class="hljs-punctuation">&#125;</span><br></code></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><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></pre></td><td class="code"><pre><code class="hljs R">f_gadem_one <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>probes<span class="hljs-punctuation">,</span> seqname<span class="hljs-punctuation">,</span> delta_start <span class="hljs-operator">=</span> <span class="hljs-number">100</span><span class="hljs-punctuation">,</span> delta_end <span class="hljs-operator">=</span> <span class="hljs-number">100</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    probes_tmp <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>probes<span class="hljs-punctuation">,</span> seqnames<span class="hljs-operator">==</span>seqname<span class="hljs-punctuation">)</span><br>    res <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><br>        seqnames <span class="hljs-operator">=</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span>seqname<span class="hljs-punctuation">,</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>probes_tmp<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>        start <span class="hljs-operator">=</span> ranges<span class="hljs-punctuation">(</span>probes_tmp<span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> as.data.frame<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> dplyr<span class="hljs-operator">::</span>pull<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;start&quot;</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">-</span> <span class="hljs-number">100</span><span class="hljs-punctuation">,</span><br>        end <span class="hljs-operator">=</span> ranges<span class="hljs-punctuation">(</span>probes_tmp<span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> as.data.frame<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> dplyr<span class="hljs-operator">::</span>pull<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;end&quot;</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> <span class="hljs-number">100</span><br>    <span class="hljs-punctuation">)</span><br>    res<br><span class="hljs-punctuation">&#125;</span><br>f_gadem <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>probes<span class="hljs-punctuation">,</span> all_seqN<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span> delta_start <span class="hljs-operator">=</span> <span class="hljs-number">100</span><span class="hljs-punctuation">,</span> delta_end <span class="hljs-operator">=</span> <span class="hljs-number">100</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">is.null</span><span class="hljs-punctuation">(</span>all_seqN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        all_seqN <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>unique<span class="hljs-punctuation">(</span>seqnames<span class="hljs-punctuation">(</span>probes<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    res_seqnames <span class="hljs-operator">&lt;-</span> <span class="hljs-literal">NULL</span><br>    res_start <span class="hljs-operator">&lt;-</span> <span class="hljs-literal">NULL</span><br>    res_end <span class="hljs-operator">&lt;-</span> <span class="hljs-literal">NULL</span><br>    <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>x <span class="hljs-keyword">in</span> all_seqN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        res <span class="hljs-operator">&lt;-</span> f_gadem_one<span class="hljs-punctuation">(</span>probes<span class="hljs-punctuation">,</span> x<span class="hljs-punctuation">,</span> delta_start<span class="hljs-punctuation">,</span> delta_end<span class="hljs-punctuation">)</span><br>        res_seqnames <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>res_seqnames<span class="hljs-punctuation">,</span> res<span class="hljs-operator">$</span>seqnames<span class="hljs-punctuation">)</span><br>        res_start <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>res_start<span class="hljs-punctuation">,</span> res<span class="hljs-operator">$</span>start<span class="hljs-punctuation">)</span><br>        res_end <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>res_end<span class="hljs-punctuation">,</span> res<span class="hljs-operator">$</span>end<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    sequence <span class="hljs-operator">&lt;-</span> GRanges<span class="hljs-punctuation">(</span><br>      seqnames <span class="hljs-operator">=</span> res_seqnames<span class="hljs-punctuation">,</span><br>      IRanges<span class="hljs-punctuation">(</span><br>        start <span class="hljs-operator">=</span> res_start<span class="hljs-punctuation">,</span><br>        end <span class="hljs-operator">=</span> res_end<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <br>      strand <span class="hljs-operator">=</span> <span class="hljs-string">&quot;*&quot;</span><br>    <span class="hljs-punctuation">)</span><br>    gadem <span class="hljs-operator">&lt;-</span> GADEM<span class="hljs-punctuation">(</span>sequence<span class="hljs-punctuation">,</span> verbose <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span> genome <span class="hljs-operator">=</span> BSgenome.Hsapiens.UCSC.hg19<span class="hljs-operator">::</span>Hsapiens<span class="hljs-punctuation">)</span><br>    gadem<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<h2 id="发现模体"><a href="#发现模体" class="headerlink" title="发现模体"></a>发现模体</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></pre></td><td class="code"><pre><code class="hljs R">saveRDS<span class="hljs-punctuation">(</span>rowRanges<span class="hljs-punctuation">(</span>res_data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;probes_hg19.rds&#x27;</span><span class="hljs-punctuation">)</span><br> <br>probes <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;probes_hg19.rds&#x27;</span><span class="hljs-punctuation">)</span><br>gadem <span class="hljs-operator">&lt;-</span> f_gadem<span class="hljs-punctuation">(</span>probes<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;chr1&#x27;</span><span class="hljs-punctuation">)</span><br>nMotifs<span class="hljs-punctuation">(</span>gadem<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 找到的模体数量</span><br>nOccurrences<span class="hljs-punctuation">(</span>gadem<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 出现的次数</span><br>consensus<span class="hljs-punctuation">(</span>gadem<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 查看模体的一致性序列</span><br><span class="hljs-comment"># 展示模体 logo 图</span><br>pwm <span class="hljs-operator">&lt;-</span> getPWM<span class="hljs-punctuation">(</span>gadem<span class="hljs-punctuation">)</span><br>pfm  <span class="hljs-operator">&lt;-</span> new<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;pfm&quot;</span><span class="hljs-punctuation">,</span>mat<span class="hljs-operator">=</span>pwm<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>name<span class="hljs-operator">=</span><span class="hljs-string">&quot;Novel Site 1&quot;</span><span class="hljs-punctuation">)</span><br>plotMotifLogo<span class="hljs-punctuation">(</span>pfm<span class="hljs-punctuation">)</span><br>saveRDS<span class="hljs-punctuation">(</span>pwm<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;chr1_pwm.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="配对分析"><a href="#配对分析" class="headerlink" title="配对分析"></a>配对分析</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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>MotIV<span class="hljs-punctuation">)</span><br>pwm <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;chr1_pwm.rds&#x27;</span><span class="hljs-punctuation">)</span><br>analysis.jaspar <span class="hljs-operator">&lt;-</span> motifMatch<span class="hljs-punctuation">(</span>pwm<span class="hljs-punctuation">)</span><br>summary<span class="hljs-punctuation">(</span>analysis.jaspar<span class="hljs-punctuation">)</span><br>options<span class="hljs-punctuation">(</span>repr.plot.width<span class="hljs-operator">=</span><span class="hljs-number">18</span><span class="hljs-punctuation">,</span> repr.plot.height<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-punctuation">)</span><br>plot<span class="hljs-punctuation">(</span>analysis.jaspar<span class="hljs-punctuation">,</span> ncol<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span> top<span class="hljs-operator">=</span><span class="hljs-number">5</span><span class="hljs-punctuation">,</span> rev<span class="hljs-operator">=</span><span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span> main<span class="hljs-operator">=</span><span class="hljs-string">&quot;&quot;</span><span class="hljs-punctuation">,</span> bysim<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span> cex<span class="hljs-operator">=</span><span class="hljs-number">0.4</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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