RunQC: QC by cell type

In nbroguiere/burgertools: Collection of tools extending the functionality of Seurat

QC by cell type

Description

This function does cell-type aware quality control for scRNA-seq data in Seurat objects. Cells listed in 'celltypes' are filtered, keeping only cells for which 'parameter' is between min.val and max.val.

Usage

RunQC(object, celltypes, parameter, min.val = 0, max.val = Inf)

Arguments

object	Seurat object. Must contain nFeature_RNA and percent.mito metadata columns, or the x and y plot parameters must be changed accordingly to plot other QC info otherwise.
celltypes	Identities that should be filtered. Must be present in Idents(object).
parameter	Metadata column on which to do the filtering.
min.val	Minimal accepted values for each identity (Default: 0).
max.val	Maximal accepted values for each identity (Default: +Inf).

Value

A Seurat object

Examples

MySeuratObject <- RunQC(MySeuratObject)

nbroguiere/burgertools documentation built on Jan. 30, 2024, 3:48 a.m.