process_seurat: Process a Seurat object

In kidcancerlab/rrrSingleCellUtils: A Set of Tools For Single Cell Analysis

Process a Seurat object

Description

Process a Seurat object

Usage

process_seurat(
  sobject,
  verbose = FALSE,
  run_umap_dims = 1:30,
  assay = "RNA",
  resolution = 0.3,
  reduction = "pca",
  graph_name = "RNA_snn",
  neighbor_k_param = 30,
  umap_n_neighbors = 30L,
  umap_metric = "euclidean"
)

Arguments

sobject	A Seurat object
verbose	Controls verbosity
run_umap_dims	Number of PCA dimensions to use in RunUMAP() and FindNeighbors()
assay	Assay to pull data for when using features, or assay used to construct Graph if running UMAP on a Graph
resolution	Value of the resolution parameter, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities.
reduction	Which dimensional reduction (PCA or ICA) to use for the UMAP input. Default is PCA
graph_name	Name of graph to use for the clustering algorithm in FindClusters()
neighbor_k_param	Number of neighbors (k.param) to use in FindNeighbors()
umap_n_neighbors	Number of neighbors (n.neighbors) to use in RunUMAP()
umap_metric	Metric (metric) to use in RunUMAP()

Value

A Seurat object

Examples

## Not run: 
test <- process_seurat(pbmc_small)

## End(Not run)

kidcancerlab/rrrSingleCellUtils documentation built on April 17, 2025, 5:10 p.m.