Skip to content

Commit

Permalink
Build site.
Browse files Browse the repository at this point in the history
  • Loading branch information
@davetang
davetang committed Oct 31, 2024
1 parent 04948c5 commit c4e09b7
Showing 1 changed file with 130 additions and 8 deletions.
138 changes: 130 additions & 8 deletions docs/edger_de.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -520,15 +520,15 @@ <h4 class="date">2024-10-31</h4>
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomdavetangmusetree92b951ca79310340c50fbcf9d3d8a59c7278a96btargetblank92b951ca">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomdavetangmusetree04948c54e3d2024b33286d089cac99d0cfbb1173targetblank04948c5a">
<span class="glyphicon glyphicon-ok text-success"
aria-hidden="true"></span> <strong>Repository version:</strong>
<a href="https://github.com/davetang/muse/tree/92b951ca79310340c50fbcf9d3d8a59c7278a96b" target="_blank">92b951c</a>
<a href="https://github.com/davetang/muse/tree/04948c54e3d2024b33286d089cac99d0cfbb1173" target="_blank">04948c5</a>
</a>
</p>
</div>
<div
id="strongRepositoryversionstrongahrefhttpsgithubcomdavetangmusetree92b951ca79310340c50fbcf9d3d8a59c7278a96btargetblank92b951ca"
id="strongRepositoryversionstrongahrefhttpsgithubcomdavetangmusetree04948c54e3d2024b33286d089cac99d0cfbb1173targetblank04948c5a"
class="panel-collapse collapse">
<div class="panel-body">
<p>
Expand All @@ -538,7 +538,7 @@ <h4 class="date">2024-10-31</h4>
</p>
<p>
The results in this page were generated with repository version
<a href="https://github.com/davetang/muse/tree/92b951ca79310340c50fbcf9d3d8a59c7278a96b" target="_blank">92b951c</a>.
<a href="https://github.com/davetang/muse/tree/04948c54e3d2024b33286d089cac99d0cfbb1173" target="_blank">04948c5</a>.
See the <em>Past versions</em> tab to see a history of the changes made
to the R Markdown and HTML files.
</p>
Expand All @@ -560,10 +560,6 @@ <h4 class="date">2024-10-31</h4>
Ignored: data/pbmc3k/
Ignored: r_packages_4.4.0/

Untracked files:
Untracked: data/13970886_edger_res.csv
Untracked: rsem.merged.gene_counts.tsv

</code></pre>
<p>
Note that any generated files, e.g. HTML, png, CSS, etc., are not
Expand Down Expand Up @@ -612,6 +608,40 @@ <h4 class="date">2024-10-31</h4>
Rmd
</td>
<td>
<a href="https://github.com/davetang/muse/blob/04948c54e3d2024b33286d089cac99d0cfbb1173/analysis/edger_de.Rmd" target="_blank">04948c5</a>
</td>
<td>
Dave Tang
</td>
<td>
2024-10-31
</td>
<td>
Export edgeR results
</td>
</tr>
<tr>
<td>
html
</td>
<td>
<a href="https://rawcdn.githack.com/davetang/muse/cfbb929582e7c0386338bce4e96900f406e7a447/docs/edger_de.html" target="_blank">cfbb929</a>
</td>
<td>
Dave Tang
</td>
<td>
2024-10-31
</td>
<td>
Build site.
</td>
</tr>
<tr>
<td>
Rmd
</td>
<td>
<a href="https://github.com/davetang/muse/blob/92b951ca79310340c50fbcf9d3d8a59c7278a96b/analysis/edger_de.Rmd" target="_blank">92b951c</a>
</td>
<td>
Expand Down Expand Up @@ -799,6 +829,48 @@ <h2>DGEList</h2>
<p>The input to <code>edgeR</code> is the <code>DGEList</code> object.
The required inputs for creating a <code>DGEList</code> object is the
count table and a grouping factor.</p>
<pre class="r"><code>gene_counts |&gt;
dplyr::select(starts_with(&quot;ERR&quot;)) |&gt;
mutate(across(everything(), as.integer)) |&gt;
as.matrix() -&gt; gene_counts_mat

row.names(gene_counts_mat) &lt;- gene_counts$gene_id

idx &lt;- match(colnames(gene_counts_mat), my_metadata$run_id)
colnames(gene_counts_mat) &lt;- my_metadata$sample[idx]

y &lt;- DGEList(
counts = gene_counts_mat,
group = my_metadata$group[idx]
)

y</code></pre>
<pre><code>An object of class &quot;DGEList&quot;
$counts
C2_norm C3_norm C5_norm C1_norm C1_cancer C2_cancer C3_cancer
ENSG00000000003 2 6 5 374 1637 650 1015
ENSG00000000005 19 40 28 0 1 0 0
ENSG00000000419 268 273 428 489 637 879 1157
ENSG00000000457 360 449 566 362 605 708 632
ENSG00000000460 155 184 264 85 312 239 147
C5_cancer
ENSG00000000003 562
ENSG00000000005 0
ENSG00000000419 729
ENSG00000000457 478
ENSG00000000460 156
63135 more rows ...

$samples
group lib.size norm.factors
C2_norm normal 4441588 1
C3_norm normal 5349291 1
C5_norm normal 7613422 1
C1_norm normal 15972904 1
C1_cancer cancer 22329493 1
C2_cancer cancer 29928921 1
C3_cancer cancer 24891206 1
C5_cancer cancer 23703606 1</code></pre>
</div>
<div id="filtering-to-remove-low-counts" class="section level2">
<h2>Filtering to remove low counts</h2>
Expand Down Expand Up @@ -845,6 +917,34 @@ <h2>Normalisation for composition bias</h2>
library size replaces the original library size in all downstream
analyses</p>
</blockquote>
<pre class="r"><code>y &lt;- normLibSizes(y)
y</code></pre>
<pre><code>An object of class &quot;DGEList&quot;
$counts
C2_norm C3_norm C5_norm C1_norm C1_cancer C2_cancer C3_cancer
ENSG00000000003 2 6 5 374 1637 650 1015
ENSG00000000005 19 40 28 0 1 0 0
ENSG00000000419 268 273 428 489 637 879 1157
ENSG00000000457 360 449 566 362 605 708 632
ENSG00000000460 155 184 264 85 312 239 147
C5_cancer
ENSG00000000003 562
ENSG00000000005 0
ENSG00000000419 729
ENSG00000000457 478
ENSG00000000460 156
37419 more rows ...

$samples
group lib.size norm.factors
C2_norm normal 4431282 1.4420477
C3_norm normal 5337400 1.4377942
C5_norm normal 7594512 1.3836402
C1_norm normal 15964680 0.8389637
C1_cancer cancer 22317658 0.8199077
C2_cancer cancer 29912740 0.7972139
C3_cancer cancer 24876336 0.8151023
C5_cancer cancer 23693355 0.7798397</code></pre>
</div>
<div id="mds" class="section level2">
<h2>MDS</h2>
Expand Down Expand Up @@ -978,6 +1078,17 @@ <h2>Differential expression</h2>
<tbody>
<tr>
<td>
<a href="https://github.com/davetang/muse/blob/cfbb929582e7c0386338bce4e96900f406e7a447/docs/figure/edger_de.Rmd/down_regulated_genes-1.png" target="_blank">cfbb929</a>
</td>
<td>
Dave Tang
</td>
<td>
2024-10-31
</td>
</tr>
<tr>
<td>
<a href="https://github.com/davetang/muse/blob/6aa4e2d485d9f744f1e0119c2d3a7aac934a1eee/docs/figure/edger_de.Rmd/down_regulated_genes-1.png" target="_blank">6aa4e2d</a>
</td>
<td>
Expand Down Expand Up @@ -1026,6 +1137,17 @@ <h2>Differential expression</h2>
<tbody>
<tr>
<td>
<a href="https://github.com/davetang/muse/blob/cfbb929582e7c0386338bce4e96900f406e7a447/docs/figure/edger_de.Rmd/up_regulated_genes-1.png" target="_blank">cfbb929</a>
</td>
<td>
Dave Tang
</td>
<td>
2024-10-31
</td>
</tr>
<tr>
<td>
<a href="https://github.com/davetang/muse/blob/6aa4e2d485d9f744f1e0119c2d3a7aac934a1eee/docs/figure/edger_de.Rmd/up_regulated_genes-1.png" target="_blank">6aa4e2d</a>
</td>
<td>
Expand Down

0 comments on commit c4e09b7

Please sign in to comment.