auto_subset: Use median and standard deviation to subset a Seurat object...

In kidcancerlab/rrrSingleCellUtils: A Set of Tools For Single Cell Analysis

Use median and standard deviation to subset a Seurat object based on specific features

Description

Use median and standard deviation to subset a Seurat object based on specific features

Usage

auto_subset(
  sobject,
  sd_down = 1,
  sd_up = 2,
  make_plots = TRUE,
  features = c("nCount_RNA", "nFeature_RNA"),
  sample_name = NULL
)

Arguments

sobject	Seurat object
sd_down	Number of standard deviations below the median to subset
sd_up	Number of standard deviations above the median to subset
make_plots	Whether to make plots of the features before and after subsetting
features	Vector of features to use for subsetting
sample_name	Name of sample to use in plot titles

Value

A Seurat object

Examples

## Not run: 
filtered <- auto_subset(SeuratObject::pbmc_small)

## End(Not run)

kidcancerlab/rrrSingleCellUtils documentation built on April 17, 2025, 5:10 p.m.