no need to add

97-git.Rmd

@@ -230,7 +230,7 @@ share it.
 
 `r msmbstyle::question_begin()`
 
-You have now been added to the
+Let now use the
 [WSBIM2122-GitHub-training](https://github.com/UCLouvain-CBIO/WSBIM2122-GitHub-training)
 repository.
 

docs/sec-git.html

@@ -465,7 +465,7 @@ <h2>
 ► Question
 </p>
 <div class="question-body">
-<p>You have now been added to the
+<p>Let now use the
 <a href="https://github.com/UCLouvain-CBIO/WSBIM2122-GitHub-training">WSBIM2122-GitHub-training</a>
 repository.</p>
 <ol style="list-style-type: decimal">

docs/sec-gsea.html

@@ -709,11 +709,11 @@ <h2>
 <pre><code>## DataFrame with 6 rows and 4 columns
 ##                Cell        Type Condition sizeFactor
 ##         &lt;character&gt; &lt;character&gt;  &lt;factor&gt;  &lt;numeric&gt;
-## sample1       Cell1  Epithelial      mock   0.726883
+## sample1       Cell1  Epithelial      KD     0.726883
 ## sample2       Cell1  Epithelial      mock   1.308664
-## sample3       Cell1  Epithelial      KD     1.077368
-## sample4       Cell1  Epithelial      KD     0.966025
-## sample5       Cell1  Epithelial      mock   1.042111
+## sample3       Cell1  Epithelial      mock   1.077368
+## sample4       Cell1  Epithelial      mock   0.966025
+## sample5       Cell1  Epithelial      KD     1.042111
 ## sample6       Cell1  Epithelial      KD     1.012664</code></pre>
 <div class="sourceCode" id="cb292"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb292-1"><a href="sec-gsea.html#cb292-1" tabindex="-1"></a>ensembl_to_geneName <span class="ot">&lt;-</span> <span class="fu">tibble</span>(<span class="at">ENSEMBL =</span> <span class="fu">rownames</span>(dds)) <span class="sc">%&gt;%</span></span>
 <span id="cb292-2"><a href="sec-gsea.html#cb292-2" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">gene =</span> AnnotationDbi<span class="sc">::</span><span class="fu">mapIds</span>(org.Hs.eg.db, ENSEMBL, <span class="st">"SYMBOL"</span>,</span>
@@ -737,22 +737,22 @@ <h2>
 <span id="cb292-20"><a href="sec-gsea.html#cb292-20" tabindex="-1"></a>    <span class="fu">mutate</span>(<span class="at">score =</span> <span class="fu">cumsum</span>(score))</span>
 <span id="cb292-21"><a href="sec-gsea.html#cb292-21" tabindex="-1"></a></span>
 <span id="cb292-22"><a href="sec-gsea.html#cb292-22" tabindex="-1"></a>res_tmp</span></code></pre></div>
-<pre><code>## # A tibble: 22,222 × 5
+<pre><code>## # A tibble: 22,223 × 5
 ##    ENSEMBL         ENTREZID   padj inGO  score
 ##    &lt;chr&gt;           &lt;chr&gt;     &lt;dbl&gt; &lt;lgl&gt; &lt;dbl&gt;
-##  1 ENSG00000278267 102466751  1.00 FALSE    -1
-##  2 ENSG00000233750 100420257  1.00 FALSE    -2
-##  3 ENSG00000228463 728481     1.00 FALSE    -3
-##  4 ENSG00000236679 728517     1.00 FALSE    -4
-##  5 ENSG00000225972 100887749  1.00 FALSE    -5
-##  6 ENSG00000225630 100652939  1.00 FALSE    -6
-##  7 ENSG00000237973 107075141  1.00 FALSE    -7
-##  8 ENSG00000229344 107075310  1.00 FALSE    -8
-##  9 ENSG00000248527 106480796  1.00 FALSE    -9
-## 10 ENSG00000198744 107075270  1.00 FALSE   -10
-## # ℹ 22,212 more rows</code></pre>
+##  1 ENSG00000278267 102466751 0.999 FALSE    -1
+##  2 ENSG00000233750 100420257 0.999 FALSE    -2
+##  3 ENSG00000236679 728517    0.999 FALSE    -3
+##  4 ENSG00000225972 100887749 0.999 FALSE    -4
+##  5 ENSG00000225630 100652939 0.999 FALSE    -5
+##  6 ENSG00000237973 107075141 0.999 FALSE    -6
+##  7 ENSG00000229344 107075310 0.999 FALSE    -7
+##  8 ENSG00000248527 106480796 0.999 FALSE    -8
+##  9 ENSG00000198744 107075270 0.999 FALSE    -9
+## 10 ENSG00000237491 105378580 0.999 FALSE   -10
+## # ℹ 22,213 more rows</code></pre>
 <div class="sourceCode" id="cb294"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb294-1"><a href="sec-gsea.html#cb294-1" tabindex="-1"></a><span class="fu">max</span>(res_tmp<span class="sc">$</span>score)</span></code></pre></div>
-<pre><code>## [1] 429.6</code></pre>
+<pre><code>## [1] 90.14634</code></pre>
 <div class="sourceCode" id="cb296"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb296-1"><a href="sec-gsea.html#cb296-1" tabindex="-1"></a><span class="fu">plot</span>(res_tmp<span class="sc">$</span>score, <span class="at">type =</span> <span class="st">"l"</span>)</span></code></pre></div>
 <p><img src="WSBIM2122_files/figure-html/gsea_res-1.png" width="672"></p>
 <p>This approach is very time consuming, given that the statistical tests

docs/sec-hts.html

@@ -706,8 +706,8 @@ <h2>
 the raw counts of each gene in that sample.</p>
 <div class="sourceCode" id="cb92"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb92-1"><a href="sec-hts.html#cb92-1" tabindex="-1"></a>counts_result <span class="ot">&lt;-</span> <span class="fu">read_tsv</span>(<span class="at">file =</span> <span class="st">"wsbim2122_data/count_data/sample1_counts.tsv.gz"</span>)</span>
 <span id="cb92-2"><a href="sec-hts.html#cb92-2" tabindex="-1"></a><span class="fu">datatable</span>(<span class="fu">head</span>(counts_result))</span></code></pre></div>
-<div class="datatables html-widget html-fill-item" id="htmlwidget-66f039debfbf4e9cda3b" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-66f039debfbf4e9cda3b">{"x":{"filter":"none","vertical":false,"data":[["1","2","3","4","5","6"],["ENSG00000223972","ENSG00000227232","ENSG00000278267","ENSG00000243485","ENSG00000284332","ENSG00000237613"],["1;1;1;1;1;1;1;1;1","1;1;1;1;1;1;1;1;1;1;1","1","1;1;1;1;1","1","1;1;1;1;1"],["11869;12010;12179;12613;12613;12975;13221;13221;13453","14404;15005;15796;16607;16858;17233;17606;17915;18268;24738;29534","17369","29554;30267;30564;30976;30976","30366","34554;35245;35277;35721;35721"],["12227;12057;12227;12721;12697;13052;13374;14409;13670","14501;15038;15947;16765;17055;17368;17742;18061;18366;24891;29570","17436","30039;30667;30667;31109;31097","30503","35174;35481;35481;36073;36081"],["+;+;+;+;+;+;+;+;+","-;-;-;-;-;-;-;-;-;-;-","-","+;+;+;+;+","+","-;-;-;-;-"],[1735,1351,68,1021,138,1219],[0,14,8,0,0,0]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Geneid<\/th>\n      <th>Chr<\/th>\n      <th>Start<\/th>\n      <th>End<\/th>\n      <th>Strand<\/th>\n      <th>Length<\/th>\n      <th>../processed_data/bam/sample1.bam<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[6,7]},{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"Geneid","targets":1},{"name":"Chr","targets":2},{"name":"Start","targets":3},{"name":"End","targets":4},{"name":"Strand","targets":5},{"name":"Length","targets":6},{"name":"../processed_data/bam/sample1.bam","targets":7}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script><div class="question">
+<div class="datatables html-widget html-fill-item" id="htmlwidget-679896369c75497097b8" style="width:100%;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-679896369c75497097b8">{"x":{"filter":"none","vertical":false,"data":[["1","2","3","4","5","6"],["ENSG00000223972","ENSG00000227232","ENSG00000278267","ENSG00000243485","ENSG00000284332","ENSG00000237613"],["1;1;1;1;1;1;1;1;1","1;1;1;1;1;1;1;1;1;1;1","1","1;1;1;1;1","1","1;1;1;1;1"],["11869;12010;12179;12613;12613;12975;13221;13221;13453","14404;15005;15796;16607;16858;17233;17606;17915;18268;24738;29534","17369","29554;30267;30564;30976;30976","30366","34554;35245;35277;35721;35721"],["12227;12057;12227;12721;12697;13052;13374;14409;13670","14501;15038;15947;16765;17055;17368;17742;18061;18366;24891;29570","17436","30039;30667;30667;31109;31097","30503","35174;35481;35481;36073;36081"],["+;+;+;+;+;+;+;+;+","-;-;-;-;-;-;-;-;-;-;-","-","+;+;+;+;+","+","-;-;-;-;-"],[1735,1351,68,1021,138,1219],[0,14,8,0,0,0]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Geneid<\/th>\n      <th>Chr<\/th>\n      <th>Start<\/th>\n      <th>End<\/th>\n      <th>Strand<\/th>\n      <th>Length<\/th>\n      <th>../processed_data/bam/sample1.bam<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[6,7]},{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"Geneid","targets":1},{"name":"Chr","targets":2},{"name":"Start","targets":3},{"name":"End","targets":4},{"name":"Strand","targets":5},{"name":"Length","targets":6},{"name":"../processed_data/bam/sample1.bam","targets":7}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script><div class="question">
 <p class="question-begin">
 ► Question
 </p>

docs/sec-linmod.html

@@ -618,8 +618,8 @@ <h2>
 some genes will increase in the mutant under dry conditions while they
 will decrease (or change to a lesser extend at least) under humid
 conditions.</p>
-<div class="datatables html-widget html-fill-item" id="htmlwidget-80570a52162c08e343e5" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-80570a52162c08e343e5">{"x":{"filter":"none","vertical":false,"data":[[1,2,3,4,5,6,7,8,9,10,11,12],["WT","WT","WT","WT","WT","WT","MT","MT","MT","MT","MT","MT"],["normal","dry","humid","normal","dry","humid","normal","dry","humid","normal","dry","humid"]],"container":"<table class=\"cell-border stripe\">\n  <thead>\n    <tr>\n      <th>sample<\/th>\n      <th>genotype<\/th>\n      <th>condition<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":12,"autoWidth":true,"columnDefs":[{"className":"dt-right","targets":0},{"name":"sample","targets":0},{"name":"genotype","targets":1},{"name":"condition","targets":2}],"order":[],"orderClasses":false,"lengthMenu":[10,12,25,50,100]}},"evals":[],"jsHooks":[]}</script><p>Such situation require a new model formula syntax</p>
+<div class="datatables html-widget html-fill-item" id="htmlwidget-9ae6d87fe684ca87027b" style="width:100%;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-9ae6d87fe684ca87027b">{"x":{"filter":"none","vertical":false,"data":[[1,2,3,4,5,6,7,8,9,10,11,12],["WT","WT","WT","WT","WT","WT","MT","MT","MT","MT","MT","MT"],["normal","dry","humid","normal","dry","humid","normal","dry","humid","normal","dry","humid"]],"container":"<table class=\"cell-border stripe\">\n  <thead>\n    <tr>\n      <th>sample<\/th>\n      <th>genotype<\/th>\n      <th>condition<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":12,"autoWidth":true,"columnDefs":[{"className":"dt-right","targets":0},{"name":"sample","targets":0},{"name":"genotype","targets":1},{"name":"condition","targets":2}],"order":[],"orderClasses":false,"lengthMenu":[10,12,25,50,100]}},"evals":[],"jsHooks":[]}</script><p>Such situation require a new model formula syntax</p>
 <div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb36-1"><a href="sec-linmod.html#cb36-1" tabindex="-1"></a><span class="sc">~</span> genotype <span class="sc">*</span> condition</span></code></pre></div>
 <p>which is equivalent to</p>
 <div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb37-1"><a href="sec-linmod.html#cb37-1" tabindex="-1"></a><span class="sc">~</span> genotype <span class="sc">+</span> condition <span class="sc">+</span> genotype <span class="sc">*</span> condition</span></code></pre></div>