scCustomize (version 3.0.1)

Add_Cell_Complexity: Add Cell Complexity

Description

Add measure of cell complexity/novelty (log10GenesPerUMI) for data QC.

Usage

Add_Cell_Complexity(object, ...)
# S3 method for liger
Add_Cell_Complexity(
  object,
  meta_col_name = "log10GenesPerUMI",
  overwrite = FALSE,
  ...
)
# S3 method for Seurat
Add_Cell_Complexity(
  object,
  meta_col_name = "log10GenesPerUMI",
  assay = "RNA",
  overwrite = FALSE,
  ...
)

Value

An object of the same class as object with columns added to object meta data.

Arguments

object

Seurat or LIGER object

...

Arguments passed to other methods

meta_col_name

name to use for new meta data column. Default is "log10GenesPerUMI".

overwrite

Logical. Whether to overwrite existing an meta.data column. Default is FALSE meaning that function will abort if column with name provided to meta_col_name is present in meta.data slot.

assay

assay to use in calculation. Default is "RNA". Note This should only be changed if storing corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).

Examples

if (FALSE) {
# Liger
liger_object <- Add_Cell_Complexity(object = liger_object)
}

# Seurat
library(Seurat)
pbmc_small <- Add_Cell_Complexity(object = pbmc_small)