Add_Cell_Complexity: Add Cell Complexity

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Add Cell Complexity

Description

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

Usage

Add_Cell_Complexity(object, ...)

## S3 method for class 'liger'
Add_Cell_Complexity(
  object,
  meta_col_name = "log10GenesPerUMI",
  overwrite = FALSE,
  ...
)

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

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).

Value

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

Examples

## Not run: 
# Liger
liger_object <- Add_Cell_Complexity(object = liger_object)

## End(Not run)

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

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.