Filter Seurat object cells by QC metrics

Filters cells based on nFeature_RNA and optional QC metrics (e.g. percent.mt, percent.rp), defined in seurat_obj@misc$qc_colnames (See QCPatternDetect). Only metrics with non-constant, non-all-zero values are used.

Usage

QCFilter(
  seurat_obj,
  data_filter.thresh = list(assay = names(seurat_obj@assays)[[1]], nFeature_thresh =
    c(200L, 6000L), nCount_thresh = c(500L, 50000L), percent.mt = 20L, percent.rp = 60L),
  verbose = TRUE,
  ...
)

Arguments

seurat_obj

A Seurat object.

data_filter.thresh

A named list with thresholds. Default: list( nFeature_thresh = c(200L, 6000L), nCount_thresh = c(500L, 25000L), percent.mt = 20L, percent.rp = 60L ).

verbose

Logical; whether to print progress messages via cli.

...

No use

Value

A filtered Seurat object.