Filter Seurat object based on QC metrics.

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 list
qc_filter_seurat_object(seu, nfeat_thresh, mito_thresh)

# S3 method for 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

C.A.Kapourani C.A.Kapourani@ed.ac.uk