process_ser: Processes counts into a Seurat object prepared for alignment.

In Chris-Cherry/sctools: Single cell analysis tools package

Description

Reads in a blank ser object (usually from 2) and processes with a traditional Seurat pipeline. By default will scale both RNA and the default assay if not RNA but will perform PCA on default assay.

Usage

process_ser(
  ser,
  mt_handle = NULL,
  mt_thresh = 0.1,
  scale_umi = TRUE,
  g2m_genes = NULL,
  s_genes = NULL,
  res = 0.8,
  other_sets = NULL,
  ref_ser = NULL,
  scale_vars = NULL
)

Arguments

ser	Seurat object to process.
mt_handle	Regex used to identify mitochondrial genes for scaling. If left blank mt gene percent will not be used to scale.
mt_thresh	Max percent of umis from mitochondrial genes for cells to be used. If mt_handle isn't used this won't have any functionality.
scale_umi	Whether or not to scale on total UMI count.
g2m_genes	Genes to use for g2m scoring and scaling. If left blank cell cycle scoring and scaling will not be done.
s_genes	Genes to use for s scoring and scaling. If left blank cell cycle scoring and scaling will not be done.
res	Resolution for clustering.
other_sets	A named list of gene sets to be used similar to percent mt for scoring and scaling. Names will appear in metadata.
ref_ser	A processed reference Seurat object used to as reference for cell selection.
scale_vars	Other features to use for scaling.

Value

Outputs a processed Seurat outputs (UMAP, Phate)

Chris-Cherry/sctools documentation built on Jan. 25, 2022, 2:19 p.m.