CopyKit-class: Placeholder for the igraph class

In navinlabcode/copykit: CopyKit

Placeholder for the igraph class

Description

S4 Class that extends the Bioconductor SingleCellExperiment class to hold single cell copy number datasets.

Usage

CopyKit(
  consensus = data.frame(),
  phylo = structure(list(), class = "phylo"),
  consensusPhylo = structure(list(), class = "phylo"),
  distMat = dist(matrix(0, 0, 0)),
  graph = igraph::graph.empty(),
  ...
)

Arguments

consensus	A data frame with the consensus information.
phylo	A phylo object with a phylogenetic tree.
consensusPhylo	A phylo object with a phylogenetic consensus tree.
graph	A graph object with a graph made from the umap data.

Value

A CopyKit class object.

Slots

phylo

Stores the single cell phylogenetic information with ape class phylo.

consensusPhylo

Stores the consensus phylogenetic information with ape class phylo.

distMat

Stores a distance matrix object used for graphs and heatmaps.

graph

Stores an igraph object for network based clustering.

consensus

stores a consensus data frame from calcConsensus.

References

The Bioconductor SingleCellExperiment Class DOI: 10.18129/B9.bioc.SingleCellExperiment

navinlabcode/copykit documentation built on Sept. 22, 2023, 9:16 a.m.