find_clusters_louvain_scExp: Build SNN graph and find cluster using Louvain Algorithm

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Build SNN graph and find cluster using Louvain Algorithm

Description

Build SNN graph and find cluster using Louvain Algorithm

Usage

find_clusters_louvain_scExp(
  scExp,
  k = 10,
  resolution = 1,
  use.dimred = "PCA",
  type = c("rank", "number", "jaccard")[3],
  BPPARAM = BiocParallel::bpparam()
)

Arguments

scExp	A SingleCellExperiment with PCA calculated
k	An integer scalar specifying the number of nearest neighbors to consider during graph construction.
resolution	A numeric specifying the resolution of clustering to pass to igraph::cluster_louvain function.
use.dimred	A string specifying the dimensionality reduction to use.
type	A string specifying the type of weighting scheme to use for shared neighbors.
BPPARAM	BPPARAM object for multiprocessing. See bpparam for more informations. Will take the default BPPARAM set in your R session.

Value

A SingleCellExperiment containing the vector of clusters (named C1, C2 ....)

Examples

data('scExp')

scExp = find_clusters_louvain_scExp(scExp, k = 10)

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.