CC-class: Correlated Clusters (CC) class definition

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

Correlated Clusters (CC) class definition

Description

The 'CC' object is a S4 object containing coefficient of correlation associated between each cluster to a phenotypic or functional variable. Moreover, this object contains parameters and results used in the statistical analysis.

Details

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

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 'identifyCC()' function.

Slots

sample.names

a character vector containing the samples used to compute correlated clusters

variable

a numeric vector containing the expression values of the associated variable

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 CC

method.adjust

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

th.correlation

a numeric value specifying the correlation threshold (R)

th.pvalue

a numeric value specifying the p-value threshold

results

a data.frame containing for each cluster (first column): the coefficient of correlation R (second column) , the associated p-value (third column) and a logical (fourth column) specifying if the cluster is significantly correlated.

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