From 0482751b6286c3751f11557f32361ca42ba58bc6 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Fri, 4 Aug 2017 15:34:17 +1000
Subject: [PATCH] Add reference index
---
_pkgdown.yml | 73 ++++++++++
docs/reference/index.html | 275 ++++++++++++++++++++++----------------
2 files changed, 230 insertions(+), 118 deletions(-)
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 886a416..d546390 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -4,3 +4,76 @@ template:
params:
bootswatch: cosmo
ganalytics: UA-52309538-4
+reference:
+ - title: Parameters
+ desc: Parameters functions and classes
+ contents:
+ - '`getParam`'
+ - '`getParams`'
+ - '`Lun2Params`'
+ - '`LunParams`'
+ - '`newParams`'
+ - '`Params`'
+ - '`SCDDParams`'
+ - '`SimpleParams`'
+ - '`SplatParams`'
+ - '`setParam`'
+ - '`setParams`'
+ - title: Estimation
+ desc: Functions for estimating parameters
+ contents:
+ - '`lun2Estimate`'
+ - '`lunEstimate`'
+ - '`scDDEstimate`'
+ - '`simpleEstimate`'
+ - '`splatEstBCV`'
+ - '`splatEstDropout`'
+ - '`splatEstimate`'
+ - '`splatEstLib`'
+ - '`splatEstMean`'
+ - '`splatEstOutlier`'
+ - title: Simulation
+ desc: Functions for simulating datasets
+ contents:
+ - '`lun2Simulate`'
+ - '`lunSimulate`'
+ - '`scDDSimulate`'
+ - '`simpleSimulate`'
+ - '`splatSimBatchCellMeans`'
+ - '`splatSimBatchEffects`'
+ - '`splatSimBCVMeans`'
+ - '`splatSimCellMeans`'
+ - '`splatSimDE`'
+ - '`splatSimDropout`'
+ - '`splatSimGeneMeans`'
+ - '`splatSimLibSizes`'
+ - '`splatSimTrueCounts`'
+ - '`splatSimulate`'
+ - title: Comparison functions
+ desc: Functions for comparing datasets
+ contents:
+ - '`compareSCESets`'
+ - '`diffSCESets`'
+ - '`makeCompPanel`'
+ - '`makeDiffPanel`'
+ - '`makeOverallPanel`'
+ - '`summariseDiff`'
+ - title: Other exported functions
+ desc: Additional functions exported by Splatter
+ contents:
+ - '`addFeatureStats`'
+ - '`addGeneLengths`'
+ - '`listSims`'
+ - title: Internals
+ desc: Internal functions and helpers
+ contents:
+ - '`bridge`'
+ - '`expandParams`'
+ - '`getLNormFactors`'
+ - '`getPathOrder`'
+ - '`logistic`'
+ - '`rbindMatched`'
+ - '`setParamsUnchecked`'
+ - '`setParamUnchecked`'
+ - '`showPP`'
+ - '`winsorize`'
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 07b46e1..19ba746 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -115,83 +115,85 @@
<tbody>
<tr>
<th colspan="2">
- <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
- <p class="section-desc"></p>
+ <h2 id="section-parameters" class="hasAnchor"><a href="#section-parameters" class="anchor"></a>Parameters</h2>
+ <p class="section-desc"><p>Parameters functions and classes</p></p>
</th>
</tr>
<tr>
<!-- -->
<td>
- <p><code><a href="addFeatureStats.html">addFeatureStats</a></code> </p>
- </td>
- <td><p>Add feature statistics</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="addGeneLengths.html">addGeneLengths</a></code> </p>
+ <p><code><a href="getParam.html">getParam</a></code> </p>
</td>
- <td><p>Add gene lengths</p></td>
+ <td><p>Get a parameter</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="bridge.html">bridge</a></code> </p>
+ <p><code><a href="getParams.html">getParams</a></code> </p>
</td>
- <td><p>Brownian bridge</p></td>
+ <td><p>Get parameters</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="compareSCESets.html">compareSCESets</a></code> </p>
+ <p></p>
</td>
- <td><p>Compare SCESet objects</p></td>
+ <td><p>The Lun2Params class</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="diffSCESets.html">diffSCESets</a></code> </p>
+ <p></p>
</td>
- <td><p>Diff SCESet objects</p></td>
+ <td><p>The LunParams class</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="expandParams.html">expandParams</a></code> </p>
+ <p><code><a href="newParams.html">newLun2Params</a></code> <code><a href="newParams.html">newLunParams</a></code> <code><a href="newParams.html">newSCDDParams</a></code> <code><a href="newParams.html">newSimpleParams</a></code> <code><a href="newParams.html">newSplatParams</a></code> </p>
</td>
- <td><p>Expand parameters</p></td>
+ <td><p>New Params</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="getLNormFactors.html">getLNormFactors</a></code> </p>
+ <p></p>
</td>
- <td><p>Get log-normal factors</p></td>
+ <td><p>The Params virtual class</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="getParam.html">getParam</a></code> </p>
+ <p></p>
</td>
- <td><p>Get a parameter</p></td>
+ <td><p>The SCDDParams class</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="getParams.html">getParams</a></code> </p>
+ <p></p>
</td>
- <td><p>Get parameters</p></td>
+ <td><p>The SimpleParams class</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="getPathOrder.html">getPathOrder</a></code> </p>
+ <p></p>
</td>
- <td><p>Get path order</p></td>
+ <td><p>The SplatParams class</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="listSims.html">listSims</a></code> </p>
+ <p><code><a href="setParam.html">setParam</a></code> </p>
</td>
- <td><p>List simulations</p></td>
+ <td><p>Set a parameter</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="logistic.html">logistic</a></code> </p>
+ <p><code><a href="setParams.html">setParams</a></code> </p>
</td>
- <td><p>Logistic function</p></td>
- </tr><tr>
+ <td><p>Set parameters</p></td>
+ </tr>
+ </tbody><tbody>
+ <tr>
+ <th colspan="2">
+ <h2 id="section-estimation" class="hasAnchor"><a href="#section-estimation" class="anchor"></a>Estimation</h2>
+ <p class="section-desc"><p>Functions for estimating parameters</p></p>
+ </th>
+ </tr>
+ <tr>
<!-- -->
<td>
<p><code><a href="lun2Estimate.html">lun2Estimate</a></code> </p>
@@ -200,249 +202,281 @@
</tr><tr>
<!-- -->
<td>
- <p></p>
+ <p><code><a href="lunEstimate.html">lunEstimate</a></code> </p>
</td>
- <td><p>The Lun2Params class</p></td>
+ <td><p>Estimate Lun simulation parameters</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="lun2Simulate.html">lun2Simulate</a></code> </p>
+ <p><code><a href="scDDEstimate.html">scDDEstimate</a></code> </p>
</td>
- <td><p>Lun2 simulation</p></td>
+ <td><p>Estimate scDD simulation parameters</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="lunEstimate.html">lunEstimate</a></code> </p>
+ <p><code><a href="simpleEstimate.html">simpleEstimate</a></code> </p>
</td>
- <td><p>Estimate Lun simulation parameters</p></td>
+ <td><p>Estimate simple simulation parameters</p></td>
</tr><tr>
<!-- -->
<td>
- <p></p>
+ <p><code><a href="splatEstBCV.html">splatEstBCV</a></code> </p>
</td>
- <td><p>The LunParams class</p></td>
+ <td><p>Estimate Splat Biological Coefficient of Variation parameters</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="lunSimulate.html">lunSimulate</a></code> </p>
+ <p><code><a href="splatEstDropout.html">splatEstDropout</a></code> </p>
</td>
- <td><p>Lun simulation</p></td>
+ <td><p>Estimate Splat dropout parameters</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="makeCompPanel.html">makeCompPanel</a></code> </p>
+ <p><code><a href="splatEstimate.html">splatEstimate</a></code> </p>
</td>
- <td><p>Make comparison panel</p></td>
+ <td><p>Estimate Splat simulation parameters</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="makeDiffPanel.html">makeDiffPanel</a></code> </p>
+ <p><code><a href="splatEstLib.html">splatEstLib</a></code> </p>
</td>
- <td><p>Make difference panel</p></td>
+ <td><p>Estimate Splat library size parameters</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="makeOverallPanel.html">makeOverallPanel</a></code> </p>
+ <p><code><a href="splatEstMean.html">splatEstMean</a></code> </p>
</td>
- <td><p>Make overall panel</p></td>
+ <td><p>Estimate Splat mean parameters</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="newParams.html">newLun2Params</a></code> <code><a href="newParams.html">newLunParams</a></code> <code><a href="newParams.html">newSCDDParams</a></code> <code><a href="newParams.html">newSimpleParams</a></code> <code><a href="newParams.html">newSplatParams</a></code> </p>
+ <p><code><a href="splatEstOutlier.html">splatEstOutlier</a></code> </p>
</td>
- <td><p>New Params</p></td>
- </tr><tr>
+ <td><p>Estimate Splat expression outlier parameters</p></td>
+ </tr>
+ </tbody><tbody>
+ <tr>
+ <th colspan="2">
+ <h2 id="section-simulation" class="hasAnchor"><a href="#section-simulation" class="anchor"></a>Simulation</h2>
+ <p class="section-desc"><p>Functions for simulating datasets</p></p>
+ </th>
+ </tr>
+ <tr>
<!-- -->
<td>
- <p></p>
+ <p><code><a href="lun2Simulate.html">lun2Simulate</a></code> </p>
</td>
- <td><p>The Params virtual class</p></td>
+ <td><p>Lun2 simulation</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="rbindMatched.html">rbindMatched</a></code> </p>
+ <p><code><a href="lunSimulate.html">lunSimulate</a></code> </p>
</td>
- <td><p>Bind rows (matched)</p></td>
+ <td><p>Lun simulation</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="scDDEstimate.html">scDDEstimate</a></code> </p>
+ <p><code><a href="scDDSimulate.html">scDDSimulate</a></code> </p>
</td>
- <td><p>Estimate scDD simulation parameters</p></td>
+ <td><p>scDD simulation</p></td>
</tr><tr>
<!-- -->
<td>
- <p></p>
+ <p><code><a href="simpleSimulate.html">simpleSimulate</a></code> </p>
</td>
- <td><p>The SCDDParams class</p></td>
+ <td><p>Simple simulation</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="scDDSimulate.html">scDDSimulate</a></code> </p>
+ <p><code><a href="splatSimBatchCellMeans.html">splatSimBatchCellMeans</a></code> </p>
</td>
- <td><p>scDD simulation</p></td>
+ <td><p>Simulate batch means</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="setParam.html">setParam</a></code> </p>
+ <p><code><a href="splatSimBatchEffects.html">splatSimBatchEffects</a></code> </p>
</td>
- <td><p>Set a parameter</p></td>
+ <td><p>Simulate batch effects</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="setParams.html">setParams</a></code> </p>
+ <p><code><a href="splatSimBCVMeans.html">splatSimBCVMeans</a></code> </p>
</td>
- <td><p>Set parameters</p></td>
+ <td><p>Simulate BCV means</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="setParamsUnchecked.html">setParamsUnchecked</a></code> </p>
+ <p><code><a href="splatSimCellMeans.html">splatSimSingleCellMeans</a></code> <code><a href="splatSimCellMeans.html">splatSimGroupCellMeans</a></code> <code><a href="splatSimCellMeans.html">splatSimPathCellMeans</a></code> </p>
</td>
- <td><p>Set parameters UNCHECKED</p></td>
+ <td><p>Simulate cell means</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="setParamUnchecked.html">setParamUnchecked</a></code> </p>
+ <p><code><a href="splatSimDE.html">splatSimGroupDE</a></code> <code><a href="splatSimDE.html">splatSimPathDE</a></code> </p>
</td>
- <td><p>Set a parameter UNCHECKED</p></td>
+ <td><p>Simulate group differential expression</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="showPP.html">showPP</a></code> </p>
+ <p><code><a href="splatSimDropout.html">splatSimDropout</a></code> </p>
</td>
- <td><p>Show pretty print</p></td>
+ <td><p>Simulate dropout</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="simpleEstimate.html">simpleEstimate</a></code> </p>
+ <p><code><a href="splatSimGeneMeans.html">splatSimGeneMeans</a></code> </p>
</td>
- <td><p>Estimate simple simulation parameters</p></td>
+ <td><p>Simulate gene means</p></td>
</tr><tr>
<!-- -->
<td>
- <p></p>
+ <p><code><a href="splatSimLibSizes.html">splatSimLibSizes</a></code> </p>
</td>
- <td><p>The SimpleParams class</p></td>
+ <td><p>Simulate library sizes</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="simpleSimulate.html">simpleSimulate</a></code> </p>
+ <p><code><a href="splatSimTrueCounts.html">splatSimTrueCounts</a></code> </p>
</td>
- <td><p>Simple simulation</p></td>
+ <td><p>Simulate true counts</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="splatEstBCV.html">splatEstBCV</a></code> </p>
+ <p><code><a href="splatSimulate.html">splatSimulate</a></code> <code><a href="splatSimulate.html">splatSimulateSingle</a></code> <code><a href="splatSimulate.html">splatSimulateGroups</a></code> <code><a href="splatSimulate.html">splatSimulatePaths</a></code> </p>
</td>
- <td><p>Estimate Splat Biological Coefficient of Variation parameters</p></td>
- </tr><tr>
+ <td><p>Splat simulation</p></td>
+ </tr>
+ </tbody><tbody>
+ <tr>
+ <th colspan="2">
+ <h2 id="section-comparison-functions" class="hasAnchor"><a href="#section-comparison-functions" class="anchor"></a>Comparison functions</h2>
+ <p class="section-desc"><p>Functions for comparing datasets</p></p>
+ </th>
+ </tr>
+ <tr>
<!-- -->
<td>
- <p><code><a href="splatEstDropout.html">splatEstDropout</a></code> </p>
+ <p><code><a href="compareSCESets.html">compareSCESets</a></code> </p>
</td>
- <td><p>Estimate Splat dropout parameters</p></td>
+ <td><p>Compare SCESet objects</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="splatEstimate.html">splatEstimate</a></code> </p>
+ <p><code><a href="diffSCESets.html">diffSCESets</a></code> </p>
</td>
- <td><p>Estimate Splat simulation parameters</p></td>
+ <td><p>Diff SCESet objects</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="splatEstLib.html">splatEstLib</a></code> </p>
+ <p><code><a href="makeCompPanel.html">makeCompPanel</a></code> </p>
</td>
- <td><p>Estimate Splat library size parameters</p></td>
+ <td><p>Make comparison panel</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="splatEstMean.html">splatEstMean</a></code> </p>
+ <p><code><a href="makeDiffPanel.html">makeDiffPanel</a></code> </p>
</td>
- <td><p>Estimate Splat mean parameters</p></td>
+ <td><p>Make difference panel</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="splatEstOutlier.html">splatEstOutlier</a></code> </p>
+ <p><code><a href="makeOverallPanel.html">makeOverallPanel</a></code> </p>
</td>
- <td><p>Estimate Splat expression outlier parameters</p></td>
+ <td><p>Make overall panel</p></td>
</tr><tr>
<!-- -->
<td>
- <p></p>
+ <p><code><a href="summariseDiff.html">summariseDiff</a></code> </p>
</td>
- <td><p>The SplatParams class</p></td>
- </tr><tr>
+ <td><p>Summarise diffSCESets</p></td>
+ </tr>
+ </tbody><tbody>
+ <tr>
+ <th colspan="2">
+ <h2 id="section-other-exported-functions" class="hasAnchor"><a href="#section-other-exported-functions" class="anchor"></a>Other exported functions</h2>
+ <p class="section-desc"><p>Additional functions exported by Splatter</p></p>
+ </th>
+ </tr>
+ <tr>
<!-- -->
<td>
- <p><code><a href="splatSimBatchCellMeans.html">splatSimBatchCellMeans</a></code> </p>
+ <p><code><a href="addFeatureStats.html">addFeatureStats</a></code> </p>
</td>
- <td><p>Simulate batch means</p></td>
+ <td><p>Add feature statistics</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="splatSimBatchEffects.html">splatSimBatchEffects</a></code> </p>
+ <p><code><a href="addGeneLengths.html">addGeneLengths</a></code> </p>
</td>
- <td><p>Simulate batch effects</p></td>
+ <td><p>Add gene lengths</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="splatSimBCVMeans.html">splatSimBCVMeans</a></code> </p>
+ <p><code><a href="listSims.html">listSims</a></code> </p>
</td>
- <td><p>Simulate BCV means</p></td>
- </tr><tr>
+ <td><p>List simulations</p></td>
+ </tr>
+ </tbody><tbody>
+ <tr>
+ <th colspan="2">
+ <h2 id="section-internals" class="hasAnchor"><a href="#section-internals" class="anchor"></a>Internals</h2>
+ <p class="section-desc"><p>Internal functions and helpers</p></p>
+ </th>
+ </tr>
+ <tr>
<!-- -->
<td>
- <p><code><a href="splatSimCellMeans.html">splatSimSingleCellMeans</a></code> <code><a href="splatSimCellMeans.html">splatSimGroupCellMeans</a></code> <code><a href="splatSimCellMeans.html">splatSimPathCellMeans</a></code> </p>
+ <p><code><a href="bridge.html">bridge</a></code> </p>
</td>
- <td><p>Simulate cell means</p></td>
+ <td><p>Brownian bridge</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="splatSimDE.html">splatSimGroupDE</a></code> <code><a href="splatSimDE.html">splatSimPathDE</a></code> </p>
+ <p><code><a href="expandParams.html">expandParams</a></code> </p>
</td>
- <td><p>Simulate group differential expression</p></td>
+ <td><p>Expand parameters</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="splatSimDropout.html">splatSimDropout</a></code> </p>
+ <p><code><a href="getLNormFactors.html">getLNormFactors</a></code> </p>
</td>
- <td><p>Simulate dropout</p></td>
+ <td><p>Get log-normal factors</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="splatSimGeneMeans.html">splatSimGeneMeans</a></code> </p>
+ <p><code><a href="getPathOrder.html">getPathOrder</a></code> </p>
</td>
- <td><p>Simulate gene means</p></td>
+ <td><p>Get path order</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="splatSimLibSizes.html">splatSimLibSizes</a></code> </p>
+ <p><code><a href="logistic.html">logistic</a></code> </p>
</td>
- <td><p>Simulate library sizes</p></td>
+ <td><p>Logistic function</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="splatSimTrueCounts.html">splatSimTrueCounts</a></code> </p>
+ <p><code><a href="rbindMatched.html">rbindMatched</a></code> </p>
</td>
- <td><p>Simulate true counts</p></td>
+ <td><p>Bind rows (matched)</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="splatSimulate.html">splatSimulate</a></code> <code><a href="splatSimulate.html">splatSimulateSingle</a></code> <code><a href="splatSimulate.html">splatSimulateGroups</a></code> <code><a href="splatSimulate.html">splatSimulatePaths</a></code> </p>
+ <p><code><a href="setParamsUnchecked.html">setParamsUnchecked</a></code> </p>
</td>
- <td><p>Splat simulation</p></td>
+ <td><p>Set parameters UNCHECKED</p></td>
</tr><tr>
<!-- -->
<td>
- <p></p>
+ <p><code><a href="setParamUnchecked.html">setParamUnchecked</a></code> </p>
</td>
- <td><p>splatter.</p></td>
+ <td><p>Set a parameter UNCHECKED</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="summariseDiff.html">summariseDiff</a></code> </p>
+ <p><code><a href="showPP.html">showPP</a></code> </p>
</td>
- <td><p>Summarise diffSCESets</p></td>
+ <td><p>Show pretty print</p></td>
</tr><tr>
<!-- -->
<td>
@@ -458,7 +492,12 @@
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
- <li><a href="#section-all-functions">All functions</a></li>
+ <li><a href="#section-parameters">Parameters</a></li>
+ <li><a href="#section-estimation">Estimation</a></li>
+ <li><a href="#section-simulation">Simulation</a></li>
+ <li><a href="#section-comparison-functions">Comparison functions</a></li>
+ <li><a href="#section-other-exported-functions">Other exported functions</a></li>
+ <li><a href="#section-internals">Internals</a></li>
</ul>
</div>
</div>
--
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