ThresholdedNanoString-class

Holds output and diagnostics from thresholdNanoString Not
intended to be called by the user.

Core data structures and methods for handling single cell assay
data.

Greg Finak

SingleCellAssay

Core data structures for single-cell assays

ThresholdedNanoString-class function

<dl class="dl-horizontal">
<dt>melted</dt><dd>A <code>data.frame</code> containing a
 melted version of <code>nsa</code>, plus the columns 'ps',
 giving the probability that a measurement belongs to the
 signal cluster, 'clusterID' the inferred cluster</dd>
 <dt>nsa</dt><dd>The thresholded <code>NanoStringAssay</code> with
 the thresholded expression in layer <code>et</code></dd>
 <dt>densities</dt><dd>A <code>list</code> of length <code>ncol(nsa)</code>
 of marginal (mixture model) densities of each gene.</dd>
 <dt>means</dt><dd>A <code>matrix</code> dimension <code>ncol(nsa)</code>
 \(\times\) 2 given the posterior mean of each cluster.</dd>
 <dt>props</dt><dd>A <code>matrix</code> dimension <code>ncol(nsa)</code>
 \(\times\) 2 given the posterior probability of each
 cluster.</dd> <dt>startLayer</dt><dd>A <code>character</code> giving the
 initial layer that was used to generate the thresholding</dd>
 </dl>

Slots

Holds output and diagnostics from thresholdNanoString
Not intended to be called by the user. — ThresholdedNanoString-class

<dl class='dl-horizontal'>
<dt>melted</dt><dd>A <code>data.frame</code> containing a
 melted version of <code>nsa</code>, plus the columns 'ps',
 giving the probability that a measurement belongs to the
 signal cluster, 'clusterID' the inferred cluster</dd>
 <dt>nsa</dt><dd>The thresholded <code>NanoStringAssay</code> with
 the thresholded expression in layer <code>et</code></dd>
 <dt>densities</dt><dd>A <code>list</code> of length <code>ncol(nsa)</code>
 of marginal (mixture model) densities of each gene.</dd>
 <dt>means</dt><dd>A <code>matrix</code> dimension <code>ncol(nsa)</code>
 \(\times\) 2 given the posterior mean of each cluster.</dd>
 <dt>props</dt><dd>A <code>matrix</code> dimension <code>ncol(nsa)</code>
 \(\times\) 2 given the posterior probability of each
 cluster.</dd> <dt>startLayer</dt><dd>A <code>character</code> giving the
 initial layer that was used to generate the thresholding</dd>
 </dl>

ThresholdedNanoString-class: Holds output and diagnostics from thresholdNanoString Not intended to be called by the user.

Description

Arguments

Slots

See Also