Skip to content

Commit

Permalink
update lect08
Browse files Browse the repository at this point in the history
  • Loading branch information
@kdkorthauer
kdkorthauer committed Feb 7, 2024
1 parent 54df8a9 commit d1db357
Show file tree
Hide file tree
Showing 3 changed files with 14 additions and 14 deletions.
16 changes: 8 additions & 8 deletions lect08-continuous/lect08-continuous.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -751,7 +751,7 @@ <h2>OLS for Multiple Linear Regression (p covariates)</h2>
</ul>
<div class="columns">
<div class="column">
<p><span class="math display">\[\small \frac{\partial S}{\partial\alpha_0}=\begin{bmatrix}
<p><span class="math display">\[\small \frac{\partial S}{\partial\boldsymbol\alpha}=\begin{bmatrix}
\frac{\partial S}{\partial\alpha_0} \\
\frac{\partial S}{\partial\alpha_1} \\
\vdots\\
Expand Down Expand Up @@ -1504,17 +1504,17 @@ <h2>OLS of first 2000 genes, using <code>lm</code> gene by gene</h2>
</div>
</div><div class="column">
<div class="cell">
<div class="sourceCode cell-code" id="cb33"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb33-1"><a href="#cb33-1"></a><span class="fu">system.time</span>(lmfits <span class="ot">&lt;-</span> allGenes <span class="sc">%&gt;%</span></span>
<div class="sourceCode cell-code" id="cb33"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb33-1"><a href="#cb33-1"></a>(t.limma <span class="ot">&lt;-</span> <span class="fu">system.time</span>(lmfits <span class="ot">&lt;-</span> allGenes <span class="sc">%&gt;%</span></span>
<span id="cb33-2"><a href="#cb33-2"></a> <span class="fu">filter</span>(gene <span class="sc">%in%</span> <span class="fu">unique</span>(allGenes<span class="sc">$</span>gene)[<span class="dv">1</span><span class="sc">:</span><span class="dv">2000</span>]) <span class="sc">%&gt;%</span></span>
<span id="cb33-3"><a href="#cb33-3"></a> <span class="fu">group_by</span>(gene) <span class="sc">%&gt;%</span> </span>
<span id="cb33-4"><a href="#cb33-4"></a> <span class="fu">group_modify</span>(<span class="sc">~</span> <span class="fu">tidy</span>(<span class="fu">lm</span>(expression <span class="sc">~</span> age <span class="sc">+</span> genotype, </span>
<span id="cb33-5"><a href="#cb33-5"></a> <span class="at">data =</span> .x))) <span class="sc">%&gt;%</span></span>
<span id="cb33-6"><a href="#cb33-6"></a> <span class="fu">select</span>(gene, term, estimate) <span class="sc">%&gt;%</span></span>
<span id="cb33-7"><a href="#cb33-7"></a> <span class="fu">pivot_wider</span>(<span class="at">names_from =</span> term, </span>
<span id="cb33-8"><a href="#cb33-8"></a> <span class="at">values_from =</span> estimate)) </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span id="cb33-8"><a href="#cb33-8"></a> <span class="at">values_from =</span> estimate)))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code> user system elapsed
4.532 0.032 4.708 </code></pre>
6.369 0.062 6.447 </code></pre>
</div>
<div class="sourceCode cell-code" id="cb35"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb35-1"><a href="#cb35-1"></a>lmfits <span class="sc">%&gt;%</span> <span class="fu">head</span>() </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
Expand All @@ -1536,11 +1536,11 @@ <h2>OLS of first 2000 genes, using <code>lm</code> gene by gene</h2>
<section id="ols-of-all-genes-at-once-using-limma" class="slide level2">
<h2>OLS of <strong>all</strong> genes at once, using <code>limma</code>:</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb37"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb37-1"><a href="#cb37-1"></a><span class="fu">system.time</span>( limmafits <span class="ot">&lt;-</span> </span>
<span id="cb37-2"><a href="#cb37-2"></a> <span class="fu">lmFit</span>(eset, <span class="fu">model.matrix</span>(<span class="sc">~</span> age <span class="sc">+</span> genotype, <span class="at">data =</span> <span class="fu">pData</span>(eset))))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="sourceCode cell-code" id="cb37"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb37-1"><a href="#cb37-1"></a>(t.ols <span class="ot">&lt;-</span> <span class="fu">system.time</span>( limmafits <span class="ot">&lt;-</span> </span>
<span id="cb37-2"><a href="#cb37-2"></a> <span class="fu">lmFit</span>(eset, <span class="fu">model.matrix</span>(<span class="sc">~</span> age <span class="sc">+</span> genotype, <span class="at">data =</span> <span class="fu">pData</span>(eset)))))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code> user system elapsed
0.121 0.034 0.155 </code></pre>
0.152 0.039 0.190 </code></pre>
</div>
<div class="sourceCode cell-code" id="cb39"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb39-1"><a href="#cb39-1"></a>limmafits<span class="sc">$</span>coefficients <span class="sc">%&gt;%</span> <span class="fu">head</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
Expand All @@ -1564,7 +1564,7 @@ <h2>OLS of <strong>all</strong> genes at once, using <code>limma</code>:</h2>
<p><strong>Tip</strong></p>
</div>
<div class="callout-content">
<p>Avoiding repetitive calculations involving <span class="math inline">\(\mathbf{X}\)</span> leads to ~30X faster computation in this example</p>
<p>Avoiding repetitive calculations involving <span class="math inline">\(\mathbf{X}\)</span> leads to ~930X faster computation in this example</p>
</div>
</div>
</div>
Expand Down
12 changes: 6 additions & 6 deletions lect08-continuous/lect08-continuous.qmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -419,7 +419,7 @@ $$=(\mathbf{y}-\mathbf{X}\boldsymbol\alpha)^T(\mathbf{y}-\mathbf{X}\boldsymbol\a

::: columns
::: column
$$\small \frac{\partial S}{\partial\alpha_0}=\begin{bmatrix}
$$\small \frac{\partial S}{\partial\boldsymbol\alpha}=\begin{bmatrix}
\frac{\partial S}{\partial\alpha_0} \\
\frac{\partial S}{\partial\alpha_1} \\
\vdots\\
Expand Down Expand Up @@ -1006,14 +1006,14 @@ allGenes %>% head(10)

::: column
```{r}
system.time(lmfits <- allGenes %>%
(t.limma <- system.time(lmfits <- allGenes %>%
filter(gene %in% unique(allGenes$gene)[1:2000]) %>%
group_by(gene) %>%
group_modify(~ tidy(lm(expression ~ age + genotype,
data = .x))) %>%
select(gene, term, estimate) %>%
pivot_wider(names_from = term,
values_from = estimate))
values_from = estimate)))
lmfits %>% head()
```
:::
Expand All @@ -1023,8 +1023,8 @@ lmfits %>% head()
## OLS of **all** genes at once, using `limma`:

```{r}
system.time( limmafits <-
lmFit(eset, model.matrix(~ age + genotype, data = pData(eset))))
(t.ols <- system.time( limmafits <-
lmFit(eset, model.matrix(~ age + genotype, data = pData(eset)))))
limmafits$coefficients %>% head()
```

Expand All @@ -1034,7 +1034,7 @@ So far, no shrinkage.


:::{.callout-tip}
Avoiding repetitive calculations involving $\mathbf{X}$ leads to ~30X faster computation in this example
Avoiding repetitive calculations involving $\mathbf{X}$ leads to ~`r signif(7.4/0.18*45101/2000,2)`X faster computation in this example
:::


Expand Down
Binary file modified lect08-continuous/lect08-continuous_files/figure-revealjs/unnamed-chunk-2-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.

0 comments on commit d1db357

Please sign in to comment.