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

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

`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.

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