Run seurat unsupervised clustering

Run seurat unsupervised clustering

Usage

RunSeuratClustering(
  object,
  RunPCAArgs = list(),
  RunUMAPArgs = list(),
  FindNeighborsArgs = list(),
  FindClustersArgs = list(),
  log = NULL,
  cache = NULL
)

Arguments

object

Seurat object

RunPCAArgs

Arguments to pass to Seurat::RunPCA()

RunUMAPArgs

Arguments to pass to Seurat::RunUMAP(). RunUMAPArgs$features can be a character vector of features directly used for UMAP, or a list with the following fields:

• order: The order of the markers to use for UMAP, e.g. "desc(abs(avg_log2FC))"

• n: The number of total features to use for UMAP, e.g. 30 If RunUMAPArgs$features is a list, it will run RunSeuratDEAnalysis() to get the markers for each group, and then select the top n/ngroups features for each group based on the order field.

FindNeighborsArgs

Arguments to pass to Seurat::FindNeighbors()

FindClustersArgs

Arguments to pass to Seurat::FindClusters()

log

Logger

cache

Directory to cache the results. Set to FALSE to disable caching

Value

The Seurat object with clustering results