CellDataSet {monocle} | R Documentation

## The CellDataSet class

### Description

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

### Details

This class is initialized from a matrix of expression values Methods that operate on CellDataSet objects constitute the basic Monocle workflow.

### Fields

`reducedDimS`

  Matrix of class numeric, containing the source values computed by Independent Components Analysis.

`reducedDimW`

  Matrix of class numeric, containing the whitened expression values computed during Independent Components Analysis.

`reducedDimA`

  Matrix of class numeric, containing the weight values computed by Independent Components Analysis.

`reducedDimK`

  A Matrix of class numeric, containing the pre-whitening matrix computed by Independent Components Analysis.

`minSpanningTree`

  An Object of class igraph, containing the minimum spanning tree used by Monocle to order cells according to progress through a biological process.

`cellPairwiseDistances`

  A Matrix of class numeric, containing the pairwise distances between cells in the reduced dimension space.

`expressionFamily`

  An Object of class vglmff, specifying the VGAM family function used for expression responses.

`lowerDetectionLimit`

  A numeric value specifying the minimum expression level considered to be true expression.

`dispFitInfo`

  An environment containing lists, one for each set of estimated dispersion values. See estimateDispersions.

`dim_reduce_type`

  A string encoding how this CellDataSet has been reduced in dimensionality

`auxOrderingData`

  An environment of auxilliary data structures used by various steps in Monocle. Not to be accessed by users directly.

[Package monocle version 2.12.0 Index]