clusterPermutationSubcluster: Performs cluster/cell type permutations to estimate an...

In edroaldo/fusca: Framework for Unified Single-Cell Analysis

Performs cluster/cell type permutations to estimate an empirical P-value.

Description

Sort cluster labels and calculate interaction with mean expression for each permutation. Save interaction to file every 1000 permutations.

Usage

clusterPermutationSubcluster(
  cellrouter,
  assay.type = "RNA",
  genelist,
  nPerm,
  interactions,
  cluster.label,
  subcluster.column = "Subpopulation",
  clusters
)

Arguments

cellrouter	CellRouter object.
assay.type	character; the type of data to use.
genelist	character vector; genes to use in the analysis.
nPerm	numeric; the number of permutations.
interactions	the interactions as calculated by the population.pairing function or the calculateObservedMean function.
cluster.label	character; column in the metadata table corresponding to the population.
subcluster.column	character; the name of the column where the subclustering information will be stored.
clusters	character; selected clusters.

Value

list; the interaction data frame for each permutation, including the columns of mean expression of ligands, receptors and pairs.

edroaldo/fusca documentation built on March 1, 2023, 1:43 p.m.