cluster_analysis_integrate_rare {CIARA}

cluster_analysis_integrate_rare

Description

cluster_analysis_integrate_rare

Usage

cluster_analysis_integrate_rare(
  raw_counts,
  project_name,
  resolution,
  neighbors,
  max_dimension,
  feature_genes = NULL
)

Arguments

raw_counts

Raw count matrix (n_genes X n_cells).

project_name

Character name of the Seurat project.

resolution

Numeric value specifying the parameter resolution used in the Seurat function FindClusters.

neighbors

Numeric value specifying the parameter k.param in the Seurat function FindNeighbors

max_dimension

Numeric value specifying the maximum number of the PCA dimensions used in the parameter dims for the Seurat function FindNeighbors

feature_genes

vector of features specifying the argument features in the Seurat function RunPCA.

Value

Seurat object including raw and normalized counts matrices, UMAP coordinates and cluster result.

Author(s)

Gabriele Lubatti [e-mail]

See Also

https://www.rdocumentation.org/packages/Seurat/versions/4.0.1/topics/FindClusters https://www.rdocumentation.org/packages/Seurat/versions/4.0.1/topics/FindNeighbors https://www.rdocumentation.org/packages/Seurat/versions/4.0.1/topics/RunPCA