stellarscope_cell_qc: Filter cells from Seurat object

In nixonlab/scopetools: What the Package Does (One Line, Title Case)

Filter cells from Seurat object

Description

This function expects that the Seurat object includes TE feature metadata. Specifically, feattype should be set to "TE" for TE features and te_class should indicate whether the TE is an "LTR" or "LINE" retroelement. Seurat objects created with load_stellarscope_seurat() will include the necessary metadata.

Usage

stellarscope_cell_qc(object)

Arguments

object

Seurat object (with TE feature metadata)

Details

The function adds metadata for the mitochondrial percentage (percent.mt), HERV percentage (percent.HERV), L1 percentage (percent.L1), and total TE percentage (percent.TE). Outliers are detected based on the median absolute deviation (MAD) implemented in scuttle::isOutlier(). Cells are excluded based on extreme RNA count, extreme feature count, or high MT percentage.

Value

Seurat object with cells passing QC

Examples

# Seurat object
pbmc <- stellarscope_cell_qc(pbmc.orig)

nixonlab/scopetools documentation built on Sept. 30, 2022, 11:15 a.m.