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Run scATAC quality control metrics

Source: R/RunATACQC.R
RunATACQC.Rd

Calculate common scATAC QC metrics and optionally filter cells by thresholds.

Usage

RunATACQC(
  srt,
  assay = NULL,
  tss.positions = NULL,
  blacklist = NULL,
  fast = TRUE,
  min_pct_reads_in_peaks = NULL,
  min_TSS_enrichment = NULL,
  max_nucleosome_signal = NULL,
  max_blacklist_ratio = NULL,
  verbose = TRUE
)

Arguments

srt

A Seurat object.

assay

Assay to use. NULL uses the default assay.

tss.positions

TSS positions passed to Signac::TSSEnrichment.

blacklist

A GRanges blacklist used to compute blacklist_ratio.

fast

Whether to use the fast mode in Signac::TSSEnrichment.

min_pct_reads_in_peaks, min_TSS_enrichment, max_nucleosome_signal, max_blacklist_ratio

Optional thresholds used for filtering cells.

verbose

Whether to print the message. Default is TRUE.

Value

A Seurat object with QC metadata added.

Examples

# \donttest{
data("pbmcmultiome_sub", package = "scop")
pbmcmultiome_sub <- RunATACQC(
  pbmcmultiome_sub,
  assay = "peaks",
  fast = TRUE
)
#> ℹ [2026-08-30 04:47:03] Calculating ATAC QC metrics...
#> ! [2026-08-30 04:47:03] Skip nucleosome signal: "No fragment files present in assay"
#> Warning: Skip nucleosome signal: "No fragment files present in assay"
#> ! [2026-08-30 04:47:03] Skip FRiP calculation: no total fragment count column or local fragments available
#> Warning: Skip FRiP calculation: no total fragment count column or local fragments available
#> ✔ [2026-08-30 04:47:03] ATAC QC completed
# }