sce_int_raw_snn_clustering_fn: Perform a fast shared nearest neighbor clustering of each...

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Perform a fast shared nearest neighbor clustering of each sample.

Description

Clustering is used for integration diagnostics.

Usage

sce_int_raw_snn_clustering_fn(
  sce_int_raw,
  snn_k = 10L,
  snn_type = "rank",
  snn_clustering_method = c("walktrap", "louvain"),
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

sce_int_raw	(input target) A named list of SingleCellExperiment objects.
snn_k	An integer scalar: number of nearest neighbors. Passed to scran::buildSNNGraph().
snn_type	A character scalar: type of weighting scheme to use for shared neighbors. Passed to scran::buildSNNGraph().
snn_clustering_method	A character scalar: type of graph clustering method: "walktrap": igraph::cluster_walktrap() "louvain": igraph::cluster_louvain()
BPPARAM	A BiocParallel::BiocParallelParam object.

Value

A list of SingleCellExperiment objects. Output target: sce_int_raw_snn_clustering

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.