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preprocess_sample: Performs an initial preprocess on a Seurat object

preprocess_sample.Rd

Conducts preliminary normalization/scaling, cell cycle scoring, and clustering on a Seurat single cell object

Usage

preprocess_sample(so_in, species, npcs_in)

Arguments

so_in

A Seurat single cell object with RNA counts

species

Species of the sample (hg38, hg19, or mm10)

npcs_in

Number of principal components to use for dimensionality reduction

Value

A Seurat single cell object with normalized read counts

Details

The function performs the following processes on the data:assay

  • Cell cycle scoring

  • Normalization and scaling of RNA counts with log normalization

  • Normalization and scaling of RNA counts with SCTransform

  • Principal components analysis, neighbor identification, UMAP dimensionality reduction and preliminary clustering (through seurat_clustering function)