Compute shared nearest neighbors (SNN) graph.

Compute shared nearest neighbors (SNN) graph.

Usage

graph_snn_fn(
  sce,
  snn_k,
  snn_type,
  dimred = "pca",
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

sce

A SingleCellExperiment object.

snn_k

An integer scalar: number of shared nearest neighbors, passed to scran::buildSNNGraph()

snn_type

A character scalar: type of weighting scheme to use for SNN, passed to scran::buildSNNGraph()

dimred

A character scalar: name of matrix in reducedDim() used to calculate SNN.

BPPARAM

A BiocParallel::BiocParallelParam object.

Value

An object of class igraph. Output target: graph_snn