small update

97-git.Rmd

@@ -102,7 +102,8 @@ repository, so that Git knows that these will need to be version
 controlled. Files that are in the working directory, but haven't been
 added to the Git repository will not be tracked. Once added, files
 aren't yet under version control, they a prepared (or *staged*) to be
-*committed*.
+*committed*. It's only upon committing that changes get versioned
+(recorded).
 
 ```{r git1, fig.cap="Version control with Git: creating a new repository.", echo=FALSE, purl=FALSE, out.width='100%', fig.align='center'}
 knitr::include_graphics("figs/git1.png")
@@ -211,8 +212,6 @@ Alice and Bastien
 - Alice can not pull to retrieve Bastien's changes from the remote.
 
 
-<!-- - Pull requests? -->
-
 ## Getting started
 
 `r msmbstyle::question_begin()`
@@ -488,7 +487,9 @@ git reset --soft HEAD~1
 
 This is only feasible on the command line.
 
-## Pull requests
+## Other Git/GitHub features of interest
+
+### Pull requests {-}
 
 There's one last operation that GitHub facilitates, which is the *pull
 request*. The use cases that we have seen above assume that all users
@@ -515,6 +516,8 @@ repository.
   as to keep everybody informed about the changes different members
   do.
 
+### Branches {-}
+
 ## Glossary and references
 
 This glossary is based on the Carpentry's [Git novice lesson

docs/sec-git.html

@@ -327,7 +327,8 @@ <h3>Git<div class="tooltip"><button class="internal-link-btn" onclick="copy_link
 controlled. Files that are in the working directory, but haven’t been
 added to the Git repository will not be tracked. Once added, files
 aren’t yet under version control, they a prepared (or <em>staged</em>) to be
-<em>committed</em>.</p>
+<em>committed</em>. It’s only upon committing that changes get versioned
+(recorded).</p>
 <div class="figure" style="text-align: center">
 <span style="display:block;" id="fig:git1"></span>
 <p class="caption marginnote shownote">

docs/sec-gsea.html

@@ -709,10 +709,10 @@ <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      KD     0.726883
+## sample1       Cell1  Epithelial      mock   0.726883
 ## sample2       Cell1  Epithelial      mock   1.308664
 ## sample3       Cell1  Epithelial      mock   1.077368
-## sample4       Cell1  Epithelial      mock   0.966025
+## sample4       Cell1  Epithelial      KD     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>
@@ -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: 22,223 × 5
-##    ENSEMBL         ENTREZID   padj inGO  score
-##    &lt;chr&gt;           &lt;chr&gt;     &lt;dbl&gt; &lt;lgl&gt; &lt;dbl&gt;
-##  1 ENSG00000278267 102466751 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>
+<pre><code>## # A tibble: 14,012 × 5
+##    ENSEMBL         ENTREZID      padj inGO  score
+##    &lt;chr&gt;           &lt;chr&gt;        &lt;dbl&gt; &lt;lgl&gt; &lt;dbl&gt;
+##  1 ENSG00000101856 10857    1.36e-147 FALSE  -1  
+##  2 ENSG00000177494 79413    5.17e- 67 FALSE  -2  
+##  3 ENSG00000136159 55270    1.83e- 44 FALSE  -3  
+##  4 ENSG00000175315 1474     9.11e- 43 FALSE  -4  
+##  5 ENSG00000128245 7533     1.87e- 42 FALSE  -5  
+##  6 ENSG00000113272 54974    9.51e- 39 FALSE  -6  
+##  7 ENSG00000213853 2013     2.00e- 36 FALSE  -7  
+##  8 ENSG00000115107 55240    1.48e- 33 FALSE  -8  
+##  9 ENSG00000008513 6482     1.17e- 32 FALSE  -9  
+## 10 ENSG00000105855 3696     3.75e- 31 TRUE   28.1
+## # ℹ 14,002 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">$</span>score)</span></code></pre></div>
-<pre><code>## [1] 90.14634</code></pre>
+<pre><code>## [1] 2155.674</code></pre>
 <div class="sourceCode" id="cb296"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb296-1"><a href="sec-gsea.html#cb296-1" tabindex="-1"></a><span class="fu">plot</span>(res_tmp<span class="sc">$</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-4d2be57fa79234c5da50" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-4d2be57fa79234c5da50">{"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-f3252cd4ee7049ab5214" style="width:100%;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-f3252cd4ee7049ab5214">{"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-c2dbebaf913ca58f2709" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-c2dbebaf913ca58f2709">{"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-86a57f2fa23644ccba8d" style="width:100%;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-86a57f2fa23644ccba8d">{"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>