CellDataSet

CellDataSet-class


The main class used by Monocle to hold single cell expression data. CellDataSet extends the basic Bioconductor ExpressionSet class.


Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data.  It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.

Cole Trapnell

monocle

Analysis tools for single-cell expression experiments.

CellDataSet function

 <dl>
   <dt><code>reducedDimS</code>:</dt><dd>Matrix of class <code>"numeric"</code>, containing the source values computed by Independent Components Analysis.</dd> <dt><code>reducedDimW</code>:</dt><dd>Matrix of class <code>"numeric"</code>, containing the whitened expression values computed during Independent Components Analysis.</dd> <dt><code>reducedDimA</code>:</dt><dd>Matrix of class <code>"numeric"</code>, containing the weight values computed by Independent Components Analysis.</dd> <dt><code>minSpanningTree</code>:</dt><dd>Object of class <code>"igraph"</code>, containing the minimum spanning tree used by Monocle to order cells according to progress through a biological process.</dd> <dt><code>cellPairwiseDistances</code>:</dt><dd>Matrix of class <code>"numeric"</code>, containing the pairwise distances between cells in the reduced dimension space.</dd> <dt><code>expressionFamily</code>:</dt><dd>Object of class <code>"vglmff"</code>, specifying the VGAM family function used for expression responses.</dd> <dt><code>lowerDetectionLimit</code>:</dt><dd>A <code>"numeric"</code> value specifying the minimum expression level considered to be true expression.</dd> </dl> 

CellDataSet: The CellDataSet class

Description

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