Runs a typical Seurat workflow on a Seurat object (up to dimensionality reduction and clustering).

Given a Seurat object, returns a new Seurat that has been normalized, had variable features identified, scaled, had principal components computed, hadclusters identified, and had tSNE and UMAP embeddings determined.

Usage

FindClustersCountsplit(
  seurat_obj,
  resolution_start = 0.8,
  reduction_percentage = 0.2,
  num_clusters_start = 20,
  dims = 1:10,
  algorithm = "louvain",
  null_method = "ZIP",
  assay = "RNA",
  cores = 1,
  shared_memory_max = 8000 * 1024^2,
  verbose = TRUE
)

Arguments

seurat_obj: The Seurat object that will be analyzed.
resolution_start: The starting resolution to be used for the clustering algorithm (Louvain and Leiden algorithms).
reduction_percentage: The amount that the starting parameter will be reduced by after each iteration (between 0 and 1).
num_clusters_start: The starting number of clusters to be used for the clustering algorithm (K-means and Hierarchical clustering algorithms).
dims: The dimensions to use as input features (i.e. 1:10).
algorithm: The clustering algorithm to be used.
null_method: The generating distribution for the synthetic null variables (ZIP, NB, ZIP-copula, NB-copula)
assay: The assay to generate artificial variables from.
cores: The number of cores to compute marker genes in parallel.
shared_memory_max: The maximum size for shared global variables. Increased this variable if you see the following error: The total size of the X globals that need to be exported for the future expression ('FUN()') is X GiB. This exceeds the maximum allowed size of 500.00 MiB (option 'future.globals.maxSize'). The X largest globals are ...
verbose: Whether or not to show all logging.

Value

Returns a Seurat object where the idents have been updated with the clusters determined via the countsplit algorithm. Latest clustering results will be stored in the object metadata under countsplit_clusters'. Note that 'countsplit_clusters' will be overwritten ever time FindClustersCountsplit is run.