cluster.ex: An example set of clusters, built using component.cluster

In PoonLab/clustuneR: Molecular clustering implementation and predictive optimization

An example set of clusters, built using component.cluster

Description

A dataset describing 5 different clusters. The headers (from alignment.ex), and associated meta data (from seq.info.ex) of cluster members is captured, as well as several cluster-level traits, such as growth and size. See component.cluster or further information onhow these were assigned based on graph.ex as an input

Usage

cluster.ex

Format

A data.table object with 9 variables:

ClusterID

The unique identifier number for this cluster. A numeric

ID

A list of vectors, each containing the accession IDs (characters) of sequences within a cluster

CollectionDate

A list of vectors, each containing the collection date of sequences within a cluster

Subtype

A list of vectors, each containing the subtypes (factors) within a cluster

Header

A list of vectors, each containing the original headers from the alignement used to build this set of clusters

Size

The original size of this cluster before being updated with new cases. This simply the number of sequences within the cluster

Growth

The growth of the cluster after new cases are added

DistThresh

The pairwise distance threshold used to create this complete set of clusters. Corresponds to a setID as an input parameter

SetID

The unique identifier for this set of clusters. A numeric

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