AP-class: Abundance Profiles (AP) class definition

In tchitchek-lab/SPADEVizR: SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

Abundance Profiles (AP) class definition

Description

The 'AP' object is a S4 object containing the information related to the cluster classification based on theirs abundance profiles. Moreover, this object contains parameters and results used in the statistical analysis.

Details

Five methods are available to classify cellular clusters: 'hierarchical_k', 'hierarchical_h', 'kmeans', 'eigencell' and 'clique'. Each method can parameterized using the 'method.parameter' parameter.

The 'print()' and 'show()' can be used to display a summary of this object. Moreover all information about this object could be saved as a tab separated file using the 'export()' method. This object is returned by the 'classifyClusteringResults()' function.

Slots

class.number

a numeric value specifying the number of clusters

cluster.size

a numeric vector containing the number of cells for each cluster

method

a character specifying the method used to classify cluster

method.parameter

a named list of parameters used by the classification method

classes

a two column dataframe with the cluster in first column and corresponding class in the second column

tchitchek-lab/SPADEVizR documentation built on Jan. 27, 2024, 8:58 p.m.