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LTLA committed Sep 1, 2024
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762 changes: 381 additions & 381 deletions docs/adt__quality__control_8hpp_source.html
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638 changes: 319 additions & 319 deletions docs/crispr__quality__control_8hpp_source.html
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12 changes: 6 additions & 6 deletions docs/index.html
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Expand Up @@ -98,7 +98,7 @@ <h1>Quick start</h1>
<div class="line">metrics.sum; <span class="comment">// vector of count sums across cells. </span></div>
<div class="line">metrics.detected; <span class="comment">// vector of detected genes across cells.</span></div>
<div class="line">metrics.subset_proportion[0]; <span class="comment">// vector of mitochondrial proportions.</span></div>
<div class="ttc" id="anamespacescran__qc_html_a11547d21005ac59afdfa595581c534bc"><div class="ttname"><a href="namespacescran__qc.html#a11547d21005ac59afdfa595581c534bc">scran_qc::compute_rna_qc_metrics</a></div><div class="ttdeci">void compute_rna_qc_metrics(const tatami::Matrix&lt; Value_, Index_ &gt; &amp;mat, const std::vector&lt; Subset_ &gt; &amp;subsets, const ComputeRnaQcMetricsBuffers&lt; Sum_, Detected_, Proportion_ &gt; &amp;output, const ComputeRnaQcMetricsOptions &amp;options)</div><div class="ttdef"><b>Definition</b> rna_quality_control.hpp:91</div></div>
<div class="ttc" id="anamespacescran__qc_html_a11547d21005ac59afdfa595581c534bc"><div class="ttname"><a href="namespacescran__qc.html#a11547d21005ac59afdfa595581c534bc">scran_qc::compute_rna_qc_metrics</a></div><div class="ttdeci">void compute_rna_qc_metrics(const tatami::Matrix&lt; Value_, Index_ &gt; &amp;mat, const std::vector&lt; Subset_ &gt; &amp;subsets, const ComputeRnaQcMetricsBuffers&lt; Sum_, Detected_, Proportion_ &gt; &amp;output, const ComputeRnaQcMetricsOptions &amp;options)</div><div class="ttdef"><b>Definition</b> rna_quality_control.hpp:92</div></div>
<div class="ttc" id="ascran__qc_8hpp_html"><div class="ttname"><a href="scran__qc_8hpp.html">scran_qc.hpp</a></div><div class="ttdoc">Simple quality control for single-cell data.</div></div>
<div class="ttc" id="astructscran__qc_1_1ComputeRnaQcMetricsOptions_html"><div class="ttname"><a href="structscran__qc_1_1ComputeRnaQcMetricsOptions.html">scran_qc::ComputeRnaQcMetricsOptions</a></div><div class="ttdoc">Options for compute_rna_qc_metrics().</div><div class="ttdef"><b>Definition</b> rna_quality_control.hpp:25</div></div>
</div><!-- fragment --><p>We can then use this to identify high-quality cells:</p>
Expand All @@ -110,8 +110,8 @@ <h1>Quick start</h1>
<div class="line">filters.get_subset_proportion()[0]; <span class="comment">// upper threshold on the mitochondrial proportion.</span></div>
<div class="line"> </div>
<div class="line"><span class="keyword">auto</span> keep = filters.filter(metrics); <span class="comment">// vector where 1 = high-quality, 0 = low-quality.</span></div>
<div class="ttc" id="anamespacescran__qc_html_af13df69a88ca429bcf8333d61bfb5802"><div class="ttname"><a href="namespacescran__qc.html#af13df69a88ca429bcf8333d61bfb5802">scran_qc::compute_rna_qc_filters</a></div><div class="ttdeci">RnaQcFilters&lt; Float_ &gt; compute_rna_qc_filters(size_t num, const ComputeRnaQcMetricsBuffers&lt; Sum_, Detected_, Proportion_ &gt; &amp;metrics, const ComputeRnaQcFiltersOptions &amp;options)</div><div class="ttdef"><b>Definition</b> rna_quality_control.hpp:476</div></div>
<div class="ttc" id="astructscran__qc_1_1ComputeRnaQcFiltersOptions_html"><div class="ttname"><a href="structscran__qc_1_1ComputeRnaQcFiltersOptions.html">scran_qc::ComputeRnaQcFiltersOptions</a></div><div class="ttdoc">Options for compute_rna_qc_filters().</div><div class="ttdef"><b>Definition</b> rna_quality_control.hpp:208</div></div>
<div class="ttc" id="anamespacescran__qc_html_af13df69a88ca429bcf8333d61bfb5802"><div class="ttname"><a href="namespacescran__qc.html#af13df69a88ca429bcf8333d61bfb5802">scran_qc::compute_rna_qc_filters</a></div><div class="ttdeci">RnaQcFilters&lt; Float_ &gt; compute_rna_qc_filters(size_t num, const ComputeRnaQcMetricsBuffers&lt; Sum_, Detected_, Proportion_ &gt; &amp;metrics, const ComputeRnaQcFiltersOptions &amp;options)</div><div class="ttdef"><b>Definition</b> rna_quality_control.hpp:477</div></div>
<div class="ttc" id="astructscran__qc_1_1ComputeRnaQcFiltersOptions_html"><div class="ttname"><a href="structscran__qc_1_1ComputeRnaQcFiltersOptions.html">scran_qc::ComputeRnaQcFiltersOptions</a></div><div class="ttdoc">Options for compute_rna_qc_filters().</div><div class="ttdef"><b>Definition</b> rna_quality_control.hpp:209</div></div>
</div><!-- fragment --><p>Users can also manually adjust the thresholds before filtering:</p>
<div class="fragment"><div class="line">filters.get_sum() = 500;</div>
<div class="line">filters.get_subset_proportion()[0] = 0.1;</div>
Expand All @@ -125,9 +125,9 @@ <h1>Quick start</h1>
<div class="line"><a class="code hl_struct" href="structscran__qc_1_1ComputeAdtQcFiltersOptions.html">scran_qc::ComputeAdtQcFiltersOptions</a> afopt;</div>
<div class="line"><span class="keyword">auto</span> afilters = <a class="code hl_function" href="namespacescran__qc.html#a4e0708c006f7362c4ca7587802293e01">scran_qc::compute_adt_qc_filters</a>(ametrics, afopt);</div>
<div class="line"><span class="keyword">auto</span> akeep = filters.filter(ametrics);</div>
<div class="ttc" id="anamespacescran__qc_html_a4e0708c006f7362c4ca7587802293e01"><div class="ttname"><a href="namespacescran__qc.html#a4e0708c006f7362c4ca7587802293e01">scran_qc::compute_adt_qc_filters</a></div><div class="ttdeci">AdtQcFilters&lt; Float_ &gt; compute_adt_qc_filters(size_t num, const ComputeAdtQcMetricsBuffers&lt; Sum_, Detected_ &gt; &amp;metrics, const ComputeAdtQcFiltersOptions &amp;options)</div><div class="ttdef"><b>Definition</b> adt_quality_control.hpp:418</div></div>
<div class="ttc" id="anamespacescran__qc_html_ac96495884db86cf7ecefb3635f649cd3"><div class="ttname"><a href="namespacescran__qc.html#ac96495884db86cf7ecefb3635f649cd3">scran_qc::compute_adt_qc_metrics</a></div><div class="ttdeci">void compute_adt_qc_metrics(const tatami::Matrix&lt; Value_, Index_ &gt; &amp;mat, const std::vector&lt; Subset_ &gt; &amp;subsets, const ComputeAdtQcMetricsBuffers&lt; Sum_, Detected_ &gt; &amp;output, const ComputeAdtQcMetricsOptions &amp;options)</div><div class="ttdef"><b>Definition</b> adt_quality_control.hpp:91</div></div>
<div class="ttc" id="astructscran__qc_1_1ComputeAdtQcFiltersOptions_html"><div class="ttname"><a href="structscran__qc_1_1ComputeAdtQcFiltersOptions.html">scran_qc::ComputeAdtQcFiltersOptions</a></div><div class="ttdoc">Options for compute_adt_qc_filters().</div><div class="ttdef"><b>Definition</b> adt_quality_control.hpp:179</div></div>
<div class="ttc" id="anamespacescran__qc_html_a4e0708c006f7362c4ca7587802293e01"><div class="ttname"><a href="namespacescran__qc.html#a4e0708c006f7362c4ca7587802293e01">scran_qc::compute_adt_qc_filters</a></div><div class="ttdeci">AdtQcFilters&lt; Float_ &gt; compute_adt_qc_filters(size_t num, const ComputeAdtQcMetricsBuffers&lt; Sum_, Detected_ &gt; &amp;metrics, const ComputeAdtQcFiltersOptions &amp;options)</div><div class="ttdef"><b>Definition</b> adt_quality_control.hpp:419</div></div>
<div class="ttc" id="anamespacescran__qc_html_ac96495884db86cf7ecefb3635f649cd3"><div class="ttname"><a href="namespacescran__qc.html#ac96495884db86cf7ecefb3635f649cd3">scran_qc::compute_adt_qc_metrics</a></div><div class="ttdeci">void compute_adt_qc_metrics(const tatami::Matrix&lt; Value_, Index_ &gt; &amp;mat, const std::vector&lt; Subset_ &gt; &amp;subsets, const ComputeAdtQcMetricsBuffers&lt; Sum_, Detected_ &gt; &amp;output, const ComputeAdtQcMetricsOptions &amp;options)</div><div class="ttdef"><b>Definition</b> adt_quality_control.hpp:92</div></div>
<div class="ttc" id="astructscran__qc_1_1ComputeAdtQcFiltersOptions_html"><div class="ttname"><a href="structscran__qc_1_1ComputeAdtQcFiltersOptions.html">scran_qc::ComputeAdtQcFiltersOptions</a></div><div class="ttdoc">Options for compute_adt_qc_filters().</div><div class="ttdef"><b>Definition</b> adt_quality_control.hpp:180</div></div>
<div class="ttc" id="astructscran__qc_1_1ComputeAdtQcMetricsOptions_html"><div class="ttname"><a href="structscran__qc_1_1ComputeAdtQcMetricsOptions.html">scran_qc::ComputeAdtQcMetricsOptions</a></div><div class="ttdoc">Options for compute_adt_qc_metrics().</div><div class="ttdef"><b>Definition</b> adt_quality_control.hpp:25</div></div>
</div><!-- fragment --><p>Once we have our filter(s), we can subset our dataset so that only the columns corresponding to high-quality cells are used for downstream analysis:</p>
<div class="fragment"><div class="line"><span class="keyword">auto</span> submatrix = <a class="code hl_functionRef" href="https://tatami-inc.github.io/tatami/namespacetatami.html#a77fad1d2a2553899a7860521d6284f50">tatami::make_DelayedSubset</a>(</div>
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