TermsClustering-class: TermsClustering class

In priesgo/TCGAome: MultiOmics (just RNAseq and RPPA...) Data Analyzer on TCGA data

Description

An S4 class to represent the dimensionality reduction computed on enrichment results. Given an object of class "GeneListEnrichment" and a distance measure this class computes: (1) the Partitioning Around Medoids (PAM) clustering (2) the cluster representative selection based on the enrichment significance and the frequency of annotation of the term to give priority to the most specific terms (3) the MultiDimensional Scaling (MDS) results on the cluster representatives

Slots

significance_threshold

The significance threshold applied to the enrichment results. The significance threshold is a fixed value, if you want to modify it you would need to create another object.

adj_method

The multiple test adjustment method. Methods supported are those supported by p.adjust()

max_clusters

The maximum number of clusters to evaluate (default: 10)

significant_results

A data.frame with the selected annotations terms after applying the multiple test correction and the significance threshold.

distance_measure

The distance measure employed for the clustering

distance_matrix

The distance matrix between annotation terms by using the given distance_measure

explained_variance

The percentage of variance explained by each MDS component

explained_variance_repr

The percentage of variance explained by each MDS component computed only to cluster representatives

silhouette

The silhouette average width for each number of clusters

priesgo/TCGAome documentation built on May 25, 2019, 11:26 a.m.