automation

R/functions.R

@@ -934,16 +934,20 @@ test.multiple <- function(Y,X,map,rho=c(0,0.5,1),spec=1,min=100,steps=20){
 #' This function ...
 #' 
 #' @param Y
-#' to do
+#' exon expression\strong{:}
+#' matrix with \eqn{n} rows (samples) and \eqn{p} columns (exons)
 #' 
 #' @param X
-#' to do
+#' SNP genotype\strong{:}
+#' matrix with \eqn{n} rows (samples) and \eqn{q} columns (SNPs)
 #' 
 #' @param map
-#' to do
+#' list with names "genes", "exons", and "snps"
+#' (output from \code{map.genes}, \code{map.exons}, and \code{map.snps})
 #'
 #' @param i
-#' to do
+#' gene index\strong{:}
+#' integer between \eqn{1} and \code{nrow(map$genes)}
 #' 
 #' @examples
 #' # see vignette
@@ -973,7 +977,7 @@ visualise <- function(Y,X,map,i){
     graphics::title(main=map$genes$gene_id[i],xlab="exons",ylab="SNPs",line=1)
     graphics::box()
     
-    # indicate gene location
+    # indicate gene location (redundant if window approx. gene)
     #snp.loc <- as.numeric(sapply(strsplit(x=colnames(X),split=":"),function(x) x[[2]]))
     #local <- which(map$genes$start[i] <= snp.loc[xs] &  snp.loc[xs] <= map$genes$end[i])
     #dx <- 1/(length(xs) - 1)

docs/articles/code.html

@@ -182,40 +182,62 @@
 <a class="sourceLine" id="cb5-8" data-line-number="8">    }</a>
 <a class="sourceLine" id="cb5-9" data-line-number="9">}</a></code></pre></div>
 <p>On the virtual machine, execute this chunk to compare the results between the Geuvadis and the BBMRI project.</p>
-<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">table &lt;-<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">chr=</span><span class="kw">seq_len</span>(<span class="dv">22</span>))</a>
-<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="cf">for</span>(i <span class="cf">in</span> <span class="kw">seq_len</span>(<span class="dv">22</span>)){</a>
-<a class="sourceLine" id="cb6-3" data-line-number="3">  <span class="co"># load p-values</span></a>
-<a class="sourceLine" id="cb6-4" data-line-number="4">  <span class="kw">load</span>(<span class="kw">file.path</span>(path,<span class="kw">paste0</span>(<span class="st">"pval.Geuvadis.chr"</span>,i,<span class="st">".RData"</span>)))</a>
-<a class="sourceLine" id="cb6-5" data-line-number="5">  a &lt;-<span class="st"> </span>pvalue; pvalue &lt;-<span class="st"> </span><span class="ot">NA</span></a>
-<a class="sourceLine" id="cb6-6" data-line-number="6">  <span class="kw">load</span>(<span class="kw">file.path</span>(path,<span class="kw">paste0</span>(<span class="st">"pval.LLS.chr"</span>,i,<span class="st">".RData"</span>)))</a>
-<a class="sourceLine" id="cb6-7" data-line-number="7">  b &lt;-<span class="st"> </span>pvalue; pvalue &lt;-<span class="st"> </span><span class="ot">NA</span></a>
-<a class="sourceLine" id="cb6-8" data-line-number="8">  </a>
-<a class="sourceLine" id="cb6-9" data-line-number="9">  <span class="co"># filter tests</span></a>
-<a class="sourceLine" id="cb6-10" data-line-number="10">  sel &lt;-<span class="st"> "rho=1"</span></a>
-<a class="sourceLine" id="cb6-11" data-line-number="11">  names &lt;-<span class="st"> </span><span class="kw">intersect</span>(<span class="kw">rownames</span>(a),<span class="kw">rownames</span>(b))</a>
-<a class="sourceLine" id="cb6-12" data-line-number="12">  a &lt;-<span class="st"> </span>a[names,sel]</a>
-<a class="sourceLine" id="cb6-13" data-line-number="13">  b &lt;-<span class="st"> </span>b[names,sel]</a>
-<a class="sourceLine" id="cb6-14" data-line-number="14">  </a>
-<a class="sourceLine" id="cb6-15" data-line-number="15">  <span class="co"># correlation</span></a>
-<a class="sourceLine" id="cb6-16" data-line-number="16">  spliceQTL<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/spliceQTL/topics/grid">grid</a></span>(<span class="dt">x=</span><span class="op">-</span><span class="kw">log</span>(a),<span class="dt">y=</span><span class="op">-</span><span class="kw">log</span>(b),<span class="dt">n=</span><span class="dv">20</span>)</a>
-<a class="sourceLine" id="cb6-17" data-line-number="17">  table<span class="op">$</span>cor[i] &lt;-<span class="st"> </span><span class="kw">round</span>(stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/cor">cor</a></span>(<span class="op">-</span><span class="kw">log</span>(a),<span class="op">-</span><span class="kw">log</span>(b),<span class="dt">method=</span><span class="st">"pearson"</span>),<span class="dt">digits=</span><span class="dv">2</span>)</a>
-<a class="sourceLine" id="cb6-18" data-line-number="18">  table<span class="op">$</span>cor.test[i] &lt;-<span class="st"> </span><span class="kw">signif</span>(stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/cor.test">cor.test</a></span>(<span class="op">-</span><span class="kw">log</span>(a),<span class="op">-</span><span class="kw">log</span>(b),<span class="dt">method=</span><span class="st">"pearson"</span>)<span class="op">$</span>p.value,<span class="dt">digits=</span><span class="dv">2</span>)</a>
-<a class="sourceLine" id="cb6-19" data-line-number="19">  </a>
-<a class="sourceLine" id="cb6-20" data-line-number="20">  <span class="co"># significance</span></a>
-<a class="sourceLine" id="cb6-21" data-line-number="21">  a &lt;-<span class="st"> </span>stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/p.adjust">p.adjust</a></span>(a)<span class="op">&lt;</span><span class="fl">0.05</span></a>
-<a class="sourceLine" id="cb6-22" data-line-number="22">  b &lt;-<span class="st"> </span>stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/p.adjust">p.adjust</a></span>(b)<span class="op">&lt;</span><span class="fl">0.05</span></a>
-<a class="sourceLine" id="cb6-23" data-line-number="23">  table<span class="op">$</span>none[i] &lt;-<span class="st"> </span><span class="kw">sum</span>(<span class="op">!</span>a <span class="op">&amp;</span><span class="st"> </span><span class="op">!</span>b)</a>
-<a class="sourceLine" id="cb6-24" data-line-number="24">  table<span class="op">$</span>GEU[i] &lt;-<span class="st"> </span><span class="kw">sum</span>(a <span class="op">&amp;</span><span class="st"> </span><span class="op">!</span>b)</a>
-<a class="sourceLine" id="cb6-25" data-line-number="25">  table<span class="op">$</span>LLS[i] &lt;-<span class="st"> </span><span class="kw">sum</span>(<span class="op">!</span>a <span class="op">&amp;</span><span class="st"> </span>b)</a>
-<a class="sourceLine" id="cb6-26" data-line-number="26">  table<span class="op">$</span>both[i] &lt;-<span class="st"> </span><span class="kw">sum</span>(a <span class="op">&amp;</span><span class="st"> </span>b)</a>
-<a class="sourceLine" id="cb6-27" data-line-number="27">  table<span class="op">$</span>chisq.test[i] &lt;-<span class="st"> </span><span class="kw">suppressWarnings</span>(<span class="kw">signif</span>(stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/chisq.test">chisq.test</a></span>(<span class="kw">table</span>(a,b))<span class="op">$</span>p.value,<span class="dt">digits=</span><span class="dv">2</span>))</a>
-<a class="sourceLine" id="cb6-28" data-line-number="28">  </a>
-<a class="sourceLine" id="cb6-29" data-line-number="29">}</a></code></pre></div>
-<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">data &lt;-<span class="st"> "LLS"</span>   <span class="co"># "Geuvadis" or "LLS"</span></a>
-<a class="sourceLine" id="cb7-2" data-line-number="2">chr &lt;-<span class="st"> </span><span class="dv">1</span>        <span class="co"># 1,2,3,...,22</span></a>
+<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">list &lt;-<span class="st"> </span><span class="kw">list</span>()</a>
+<a class="sourceLine" id="cb6-2" data-line-number="2">table &lt;-<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">chr=</span><span class="kw">seq_len</span>(<span class="dv">22</span>))</a>
+<a class="sourceLine" id="cb6-3" data-line-number="3"><span class="cf">for</span>(i <span class="cf">in</span> <span class="kw">seq_len</span>(<span class="dv">22</span>)){</a>
+<a class="sourceLine" id="cb6-4" data-line-number="4">  <span class="co"># load p-values</span></a>
+<a class="sourceLine" id="cb6-5" data-line-number="5">  <span class="kw">load</span>(<span class="kw">file.path</span>(path,<span class="kw">paste0</span>(<span class="st">"pval.Geuvadis.chr"</span>,i,<span class="st">".RData"</span>)))</a>
+<a class="sourceLine" id="cb6-6" data-line-number="6">  a &lt;-<span class="st"> </span>pvalue; pvalue &lt;-<span class="st"> </span><span class="ot">NA</span></a>
+<a class="sourceLine" id="cb6-7" data-line-number="7">  <span class="kw">load</span>(<span class="kw">file.path</span>(path,<span class="kw">paste0</span>(<span class="st">"pval.LLS.chr"</span>,i,<span class="st">".RData"</span>)))</a>
+<a class="sourceLine" id="cb6-8" data-line-number="8">  b &lt;-<span class="st"> </span>pvalue; pvalue &lt;-<span class="st"> </span><span class="ot">NA</span></a>
+<a class="sourceLine" id="cb6-9" data-line-number="9">  </a>
+<a class="sourceLine" id="cb6-10" data-line-number="10">  <span class="co"># filter tests</span></a>
+<a class="sourceLine" id="cb6-11" data-line-number="11">  sel &lt;-<span class="st"> "rho=1"</span></a>
+<a class="sourceLine" id="cb6-12" data-line-number="12">  names &lt;-<span class="st"> </span><span class="kw">intersect</span>(<span class="kw">rownames</span>(a),<span class="kw">rownames</span>(b))</a>
+<a class="sourceLine" id="cb6-13" data-line-number="13">  a &lt;-<span class="st"> </span>a[names,sel]</a>
+<a class="sourceLine" id="cb6-14" data-line-number="14">  b &lt;-<span class="st"> </span>b[names,sel]</a>
+<a class="sourceLine" id="cb6-15" data-line-number="15">  </a>
+<a class="sourceLine" id="cb6-16" data-line-number="16">  <span class="co">#graphics::plot.new()</span></a>
+<a class="sourceLine" id="cb6-17" data-line-number="17">  <span class="co">#graphics::plot.window(xlim=c(0.5,length(a)+0.5),ylim=c(-1,1)*max(c(a,b)))</span></a>
+<a class="sourceLine" id="cb6-18" data-line-number="18">  <span class="co">#graphics::box()</span></a>
+<a class="sourceLine" id="cb6-19" data-line-number="19">  <span class="co">#graphics::axis(side=1)</span></a>
+<a class="sourceLine" id="cb6-20" data-line-number="20">  <span class="co">#graphics::axis(side=2)</span></a>
+<a class="sourceLine" id="cb6-21" data-line-number="21">  <span class="co">#graphics::points(a,col="red")</span></a>
+<a class="sourceLine" id="cb6-22" data-line-number="22">  <span class="co">#graphics::segments(x0=seq_along(a),y0=0,y1=a,col="red")</span></a>
+<a class="sourceLine" id="cb6-23" data-line-number="23">  <span class="co">#graphics::points(-b,col="blue")</span></a>
+<a class="sourceLine" id="cb6-24" data-line-number="24">  <span class="co">#graphics::segments(x0=seq_along(b),y0=0,y1=-b,col="blue")</span></a>
+<a class="sourceLine" id="cb6-25" data-line-number="25">  <span class="co">#graphics::abline(h=0,col="grey")</span></a>
+<a class="sourceLine" id="cb6-26" data-line-number="26">  </a>
+<a class="sourceLine" id="cb6-27" data-line-number="27">  <span class="co"># correlation</span></a>
+<a class="sourceLine" id="cb6-28" data-line-number="28">  file &lt;-<span class="st"> </span><span class="kw">file.path</span>(path,<span class="st">"plots"</span>,<span class="kw">paste0</span>(<span class="st">"cor.chr"</span>,i,<span class="st">".pdf"</span>))</a>
+<a class="sourceLine" id="cb6-29" data-line-number="29">  grDevices<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/grDevices/topics/pdf">pdf</a></span>(<span class="dt">file=</span>file,<span class="dt">width=</span><span class="dv">4</span>,<span class="dt">height=</span><span class="dv">4</span>)</a>
+<a class="sourceLine" id="cb6-30" data-line-number="30">  spliceQTL<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/spliceQTL/topics/grid">grid</a></span>(<span class="dt">x=</span><span class="op">-</span><span class="kw">log</span>(a),<span class="dt">y=</span><span class="op">-</span><span class="kw">log</span>(b),<span class="dt">n=</span><span class="dv">20</span>)</a>
+<a class="sourceLine" id="cb6-31" data-line-number="31">  grDevices<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/grDevices/topics/dev">dev.off</a></span>()</a>
+<a class="sourceLine" id="cb6-32" data-line-number="32">  table<span class="op">$</span>cor[i] &lt;-<span class="st"> </span><span class="kw">round</span>(stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/cor">cor</a></span>(<span class="op">-</span><span class="kw">log</span>(a),<span class="op">-</span><span class="kw">log</span>(b),<span class="dt">method=</span><span class="st">"pearson"</span>),<span class="dt">digits=</span><span class="dv">2</span>)</a>
+<a class="sourceLine" id="cb6-33" data-line-number="33">  table<span class="op">$</span>cor.test[i] &lt;-<span class="st"> </span><span class="kw">signif</span>(stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/cor.test">cor.test</a></span>(<span class="op">-</span><span class="kw">log</span>(a),<span class="op">-</span><span class="kw">log</span>(b),<span class="dt">method=</span><span class="st">"pearson"</span>)<span class="op">$</span>p.value,<span class="dt">digits=</span><span class="dv">2</span>)</a>
+<a class="sourceLine" id="cb6-34" data-line-number="34">  </a>
+<a class="sourceLine" id="cb6-35" data-line-number="35">  <span class="co"># significance</span></a>
+<a class="sourceLine" id="cb6-36" data-line-number="36">  a &lt;-<span class="st"> </span>stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/p.adjust">p.adjust</a></span>(a)<span class="op">&lt;</span><span class="fl">0.05</span></a>
+<a class="sourceLine" id="cb6-37" data-line-number="37">  b &lt;-<span class="st"> </span>stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/p.adjust">p.adjust</a></span>(b)<span class="op">&lt;</span><span class="fl">0.05</span></a>
+<a class="sourceLine" id="cb6-38" data-line-number="38">  table<span class="op">$</span>none[i] &lt;-<span class="st"> </span><span class="kw">sum</span>(<span class="op">!</span>a <span class="op">&amp;</span><span class="st"> </span><span class="op">!</span>b)</a>
+<a class="sourceLine" id="cb6-39" data-line-number="39">  table<span class="op">$</span>onlyGEU[i] &lt;-<span class="st"> </span><span class="kw">sum</span>(a <span class="op">&amp;</span><span class="st"> </span><span class="op">!</span>b)</a>
+<a class="sourceLine" id="cb6-40" data-line-number="40">  table<span class="op">$</span>onlyLLS[i] &lt;-<span class="st"> </span><span class="kw">sum</span>(<span class="op">!</span>a <span class="op">&amp;</span><span class="st"> </span>b)</a>
+<a class="sourceLine" id="cb6-41" data-line-number="41">  table<span class="op">$</span>both[i] &lt;-<span class="st"> </span><span class="kw">sum</span>(a <span class="op">&amp;</span><span class="st"> </span>b)</a>
+<a class="sourceLine" id="cb6-42" data-line-number="42">  table<span class="op">$</span>chisq.test[i] &lt;-<span class="st"> </span><span class="kw">suppressWarnings</span>(<span class="kw">signif</span>(stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/chisq.test">chisq.test</a></span>(<span class="kw">table</span>(a,b))<span class="op">$</span>p.value,<span class="dt">digits=</span><span class="dv">2</span>))</a>
+<a class="sourceLine" id="cb6-43" data-line-number="43">  </a>
+<a class="sourceLine" id="cb6-44" data-line-number="44">  list[[i]] &lt;-<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">chr=</span>i,<span class="dt">gene=</span><span class="kw">names</span>(a),<span class="dt">Geuvadis=</span><span class="dv">1</span><span class="op">*</span>a,<span class="dt">LLS=</span><span class="dv">1</span><span class="op">*</span>b,<span class="dt">row.names=</span><span class="kw">seq_along</span>(a))</a>
+<a class="sourceLine" id="cb6-45" data-line-number="45">  </a>
+<a class="sourceLine" id="cb6-46" data-line-number="46">}</a>
+<a class="sourceLine" id="cb6-47" data-line-number="47">list &lt;-<span class="st"> </span><span class="kw">do.call</span>(<span class="dt">what=</span><span class="st">"rbind"</span>,<span class="dt">args=</span>list)</a>
+<a class="sourceLine" id="cb6-48" data-line-number="48"><span class="kw">save</span>(list,<span class="dt">file=</span><span class="st">"list.RData"</span>)</a>
+<a class="sourceLine" id="cb6-49" data-line-number="49"><span class="kw">save</span>(table,<span class="dt">file=</span><span class="st">"table.RData"</span>)</a></code></pre></div>
+<p>On the virtual machine, execute this chunk to plot correlations between SNPs and exons (unclear which genes should be examined).</p>
+<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">data &lt;-<span class="st"> "LLS"</span> <span class="co"># "Geuvadis" or "LLS"</span></a>
+<a class="sourceLine" id="cb7-2" data-line-number="2">chr &lt;-<span class="st"> </span><span class="dv">22</span> <span class="co"># 1,2,3,...,22</span></a>
 <a class="sourceLine" id="cb7-3" data-line-number="3"><span class="kw">load</span>(<span class="kw">file.path</span>(path,<span class="kw">paste0</span>(<span class="st">"temp."</span>,data,<span class="st">".chr"</span>,chr,<span class="st">".RData"</span>)))</a>
-<a class="sourceLine" id="cb7-4" data-line-number="4">i &lt;-<span class="st"> </span><span class="kw">which</span>(map<span class="op">$</span>genes<span class="op">$</span>gene_id<span class="op">==</span><span class="st">"ENSG00000116171"</span>)</a>
-<a class="sourceLine" id="cb7-5" data-line-number="5"><span class="kw"><a href="../reference/visualise.html">visualise</a></span>(<span class="dt">Y=</span>exons,<span class="dt">X=</span>snps,<span class="dt">map=</span>map,<span class="dt">i=</span>i)</a></code></pre></div>
+<a class="sourceLine" id="cb7-4" data-line-number="4"><span class="co"># id &lt;- sample(names(a)[...],size=1) # significance (e.g. a &amp; b)</span></a>
+<a class="sourceLine" id="cb7-5" data-line-number="5"><span class="co"># i &lt;- which(map$genes$gene_id=="...") # gene name (e.g. ENSG00000172967)</span></a>
+<a class="sourceLine" id="cb7-6" data-line-number="6">spliceQTL<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/spliceQTL/topics/visualise">visualise</a></span>(<span class="dt">Y=</span>exons,<span class="dt">X=</span>snps,<span class="dt">map=</span>map,<span class="dt">i=</span>i)</a></code></pre></div>
 <!--
 #wait <- TRUE
 #while(wait){

docs/reference/visualise.html

@@ -130,19 +130,23 @@
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>Y</th>
-      <td><p>to do</p></td>
+      <td><p>exon expression<strong>:</strong>
+matrix with \(n\) rows (samples) and \(p\) columns (exons)</p></td>
     </tr>
     <tr>
       <th>X</th>
-      <td><p>to do</p></td>
+      <td><p>SNP genotype<strong>:</strong>
+matrix with \(n\) rows (samples) and \(q\) columns (SNPs)</p></td>
     </tr>
     <tr>
       <th>map</th>
-      <td><p>to do</p></td>
+      <td><p>list with names "genes", "exons", and "snps"
+(output from <code>map.genes</code>, <code>map.exons</code>, and <code>map.snps</code>)</p></td>
     </tr>
     <tr>
       <th>i</th>
-      <td><p>to do</p></td>
+      <td><p>gene index<strong>:</strong>
+integer between \(1\) and <code>nrow(map$genes)</code></p></td>
     </tr>
     </table>
     

man/visualise.Rd

@@ -7,13 +7,17 @@
 visualise(Y, X, map, i)
 }
 \arguments{
-\item{Y}{to do}
+\item{Y}{exon expression\strong{:}
+matrix with \eqn{n} rows (samples) and \eqn{p} columns (exons)}
 
-\item{X}{to do}
+\item{X}{SNP genotype\strong{:}
+matrix with \eqn{n} rows (samples) and \eqn{q} columns (SNPs)}
 
-\item{map}{to do}
+\item{map}{list with names "genes", "exons", and "snps"
+(output from \code{map.genes}, \code{map.exons}, and \code{map.snps})}
 
-\item{i}{to do}
+\item{i}{gene index\strong{:}
+integer between \eqn{1} and \code{nrow(map$genes)}}
 }
 \description{
 This function ...

vignettes/code.Rmd

@@ -119,6 +119,7 @@ for(chr in 22:1){ # 22:1
 On the virtual machine, execute this chunk to compare the results between the Geuvadis and the BBMRI project.
 
 ```{r,eval=FALSE}
+list <- list()
 table <- data.frame(chr=seq_len(22))
 for(i in seq_len(22)){
   # load p-values
@@ -133,8 +134,22 @@ for(i in seq_len(22)){
   a <- a[names,sel]
   b <- b[names,sel]
   
+  #graphics::plot.new()
+  #graphics::plot.window(xlim=c(0.5,length(a)+0.5),ylim=c(-1,1)*max(c(a,b)))
+  #graphics::box()
+  #graphics::axis(side=1)
+  #graphics::axis(side=2)
+  #graphics::points(a,col="red")
+  #graphics::segments(x0=seq_along(a),y0=0,y1=a,col="red")
+  #graphics::points(-b,col="blue")
+  #graphics::segments(x0=seq_along(b),y0=0,y1=-b,col="blue")
+  #graphics::abline(h=0,col="grey")
+  
   # correlation
+  file <- file.path(path,"plots",paste0("cor.chr",i,".pdf"))
+  grDevices::pdf(file=file,width=4,height=4)
   spliceQTL::grid(x=-log(a),y=-log(b),n=20)
+  grDevices::dev.off()
   table$cor[i] <- round(stats::cor(-log(a),-log(b),method="pearson"),digits=2)
   table$cor.test[i] <- signif(stats::cor.test(-log(a),-log(b),method="pearson")$p.value,digits=2)
   
@@ -142,26 +157,31 @@ for(i in seq_len(22)){
   a <- stats::p.adjust(a)<0.05
   b <- stats::p.adjust(b)<0.05
   table$none[i] <- sum(!a & !b)
-  table$GEU[i] <- sum(a & !b)
-  table$LLS[i] <- sum(!a & b)
+  table$onlyGEU[i] <- sum(a & !b)
+  table$onlyLLS[i] <- sum(!a & b)
   table$both[i] <- sum(a & b)
   table$chisq.test[i] <- suppressWarnings(signif(stats::chisq.test(table(a,b))$p.value,digits=2))
   
+  list[[i]] <- data.frame(chr=i,gene=names(a),Geuvadis=1*a,LLS=1*b,row.names=seq_along(a))
+  
 }
+list <- do.call(what="rbind",args=list)
+save(list,file="list.RData")
+save(table,file="table.RData")
 ```
 
+On the virtual machine, execute this chunk to plot correlations between SNPs and exons (unclear which genes should be examined).
 
 ```{r,eval=FALSE}
-data <- "LLS"   # "Geuvadis" or "LLS"
-chr <- 1        # 1,2,3,...,22
+data <- "LLS" # "Geuvadis" or "LLS"
+chr <- 22 # 1,2,3,...,22
 load(file.path(path,paste0("temp.",data,".chr",chr,".RData")))
-i <- which(map$genes$gene_id=="ENSG00000116171")
-visualise(Y=exons,X=snps,map=map,i=i)
+# id <- sample(names(a)[...],size=1) # significance (e.g. a & b)
+# i <- which(map$genes$gene_id=="...") # gene name (e.g. ENSG00000172967)
+spliceQTL::visualise(Y=exons,X=snps,map=map,i=i)
 ```
 
 
-
-
 <!--
 #wait <- TRUE
 #while(wait){