Perform a fast shared nearest neighbor clustering of each sample. — sce_int_raw_snn_clustering

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