getExtraneousCladeSubpopulations: Calculates subpopulations in clades (with two or more...

In PAC: Partition-Assisted Clustering and Multiple Alignments of Networks

Description

Calculates subpopulations in clades (with two or more subpopulations) that are too far away from other subpopulations (within the same clade) on the constellation plot; these far away subpopulations should be pruned away from the original clades.

Usage

getExtraneousCladeSubpopulations(tsneResults, pacman_results,
  threshold_multiplier, max_threshold)

Arguments

tsneResults	t-SNE output of clade centroids' embedding.
pacman_results	PAC-MAN analysis result matrix that contains network annotation, clade IDs and mean (centroid) clade expression levels.
threshold_multiplier	how many times the threshold ( (a) spread from center of clade for clades with three or more sample subpopulations and (b) distance from each subpopulation centroid for clades with exactly two subpopulations).
max_threshold	the maximum distance (on t-SNE plane) allowed for sample subpopulations to be categorized into the same clade.

Value

Returns clade subpopulations to be pruned.

PAC documentation built on Feb. 18, 2021, 9:06 a.m.