AC-class: Abundant Clusters (AC) class definition

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

Abundant Clusters (AC) class definition

Description

The 'AC' object is a S4 object containing the information related to the abundant clusters in a given biological condition. Moreover, this object contains parameters and results used in the statistical analysis.

Details

A cluster is considered as a significant abundant cluster if its associated p-value and mean are below the specific thresholds 'th.pvalue'.

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 'identifyAC()' function.

Slots

sample.names

a character vector containing the samples used to compute the abundant clusters

cluster.size

a numeric vector containing the number of cells for each cluster

use.percentages

a logical specifying if computation was performed on percentage of cell abundance

method

a character containing the name of the statistical test used to identify the abundant clusters

method.adjust

a character containing the name of the multiple correction method used (if any)

mu

a numeric specifying the theoretical value of the one sample statistical test

th.pvalue

a numeric value specifying the p-value threshold

results

a data.frame containing for each cluster (first column): the mean (second column) and the standard deviation (third column) of the biological condition, the associated p-value (fourth column) and a logical (fifth column) specifying if the cluster is significantly abundant.

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