mono.pat.cluster: Obtain monophyletic clusters based on pairwise distances

In PoonLab/clustuneR: Molecular clustering implementation and predictive optimization

Obtain monophyletic clusters based on pairwise distances

Description

Clusters are defined as as a monophyletic clade under a high-confidence common ancestor. Some measure of divergence (criterion) within this clade must fall under a distance threshold in order for it to be labelled a cluster.

Usage

mono.pat.cluster(
  t,
  dist.thresh,
  boot.thresh = 0,
  dist.criterion = "max.patristic.dist",
  setID = 0
)

Arguments

t:	The input tree file, annotated with vertex and edge information
dist.criterion:	A particular column in node.info that must be less than a distance threshold. By default, this is "max.patristic.dist", however, the "mean.patristic.dist" is also a column. Other columns added to node.info can be checked against dist.thresh, however, these would be added by the user.
dist.thresh:	The threshold required for clustering. Monophyletic groups with criterion under this value could be considered clusters.
setID:	A numeric identifier for this cluster set.
boot.thresh:	The minimum bootstrap threshold defining clusters. Monophyletic groups with a parent node more certain than this criterion could be considered clusters

Value

: A set of clusters as a data.table. See example cluster.ex object documentation for an example of clustered sequence data + meta data

PoonLab/clustuneR documentation built on Jan. 29, 2024, 2:40 a.m.