qc_filter_seurat_object: Filter Seurat object based on QC metrics.

In andreaskapou/SeuratPipe: Packaging common Seurat analysis tasks

Filter Seurat object based on QC metrics.

Description

This function filters a Seurat object (i.e. removes cells) based on QC metric thresholds. For now only based on nFeatures and mitochondrial percentage.

Usage

qc_filter_seurat_object(seu, nfeat_thresh, mito_thresh)

## S3 method for class 'list'
qc_filter_seurat_object(seu, nfeat_thresh, mito_thresh)

## S3 method for class 'Seurat'
qc_filter_seurat_object(seu, nfeat_thresh, mito_thresh)

Arguments

seu	Seurat object or list of Seurat objects(required).
nfeat_thresh	Filter cells that have less than 'nfeat_thresh' counts expressed.
mito_thresh	Filter cells with more than 'mito_thresh'% counts.

Value

List of QC filtered Seurat objects. If a single sample, returns a QC filtered Seurat object instead of a list.

Author(s)

C.A.Kapourani [e-mail]

andreaskapou/SeuratPipe documentation built on Nov. 22, 2022, 4:16 p.m.