Add reference index

_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`'

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>