Calculate QC metrics (UMIs, genes, mito%, MALAT1, stress; optional splicing metrics) Computes nCount/nFeature, pctMT, MALAT1 fraction, stress_score (case-insensitive SYMBOL match), and optional splicing metrics from same object layers or external Seurat objects. Compatible with Seurat v5 layers and v4 slots. Returns a data.frame and (if add_to_meta=TRUE) writes *_QC fields into obj@meta.data (no regression in field names).

Calculate QC metrics (UMIs, genes, mito%, MALAT1, stress; optional splicing metrics) Computes nCount/nFeature, pctMT, MALAT1 fraction, stress_score (case-insensitive SYMBOL match), and optional splicing metrics from same object layers or external Seurat objects. Compatible with Seurat v5 layers and v4 slots. Returns a data.frame and (if add_to_meta=TRUE) writes *_QC fields into obj@meta.data (no regression in field names).

Usage

calcQCmetrics(
  obj,
  assay = "RNA",
  slot = "counts",
  species = c("mouse", "human"),
  spliced = NULL,
  unspliced = NULL,
  spliced_obj = NULL,
  spliced_assay = NULL,
  spliced_layer = "counts",
  unspliced_obj = NULL,
  unspliced_assay = NULL,
  unspliced_layer = "counts",
  add_to_meta = TRUE,
  debug = getOption("scQCenrich.debug", FALSE)
)

Arguments

obj

Seurat object

assay

assay name (default "RNA")

slot

for v4 compatibility ("counts"); ignored when layer is used internally

species

"mouse" or "human"

spliced, unspliced

optional layer spec within same object; either a single layer string (e.g., "spliced") or "assay:layer" (e.g., "spliced:counts"). Ignored if external objects are provided.

spliced_obj, unspliced_obj

optional external Seurat objects

spliced_assay, unspliced_assay

assay names on external objects

spliced_layer, unspliced_layer

layer names on external objects (e.g., "counts")

add_to_meta

write *_QC back to obj@meta.data

debug

logical; defaults to options(scQCenrich.debug, FALSE)