CellDataSet: The CellDataSet class

In cole-trapnell-lab/monocle-release: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

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.

cole-trapnell-lab/monocle-release documentation built on May 13, 2019, 8:50 p.m.