graph_snn_fn: Compute shared nearest neighbors (SNN) graph.

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

Compute shared nearest neighbors (SNN) graph.

Description

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

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