Run doublet-calling with Scrublet

Usage

RunScrublet(
  srt,
  assay = "RNA",
  db_rate = ncol(srt)/1000 * 0.01,
  data_type = NULL,
  ...,
  verbose = TRUE
)

Arguments

srt: A Seurat object.
assay: Assay used for doublet calling.
db_rate: Expected doublet rate.
data_type: Optional CheckDataType result, used internally to avoid rescanning the count matrix.
...: Additional arguments to be passed to scrublet.Scrublet.
verbose: Whether to print messages.

Examples

data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
#> ℹ [2026-08-30 05:36:28] Start standard processing workflow...
#> ℹ [2026-08-30 05:36:28] Checking a list of <Seurat>...
#> ! [2026-08-30 05:36:28] Data 1/1 of the `srt_list` is "unknown"
#> Warning: Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-08-30 05:36:28] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 05:36:28] Perform `FindVariableFeatures()` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 05:36:28] Use the separate HVF from `srt_list`
#> ℹ [2026-08-30 05:36:29] Number of available HVF: 2000
#> ℹ [2026-08-30 05:36:29] Finished check
#> ℹ [2026-08-30 05:36:29] Perform `ScaleData()`
#> ℹ [2026-08-30 05:36:29] Perform pca linear dimension reduction
#> ℹ [2026-08-30 05:36:29] Use stored estimated dimensions 1:23 for Standardpca
#> ℹ [2026-08-30 05:36:29] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-08-30 05:36:30] Reorder clusters...
#> ℹ [2026-08-30 05:36:30] Skip `log1p()` because `layer = data` is not "counts"
#> ℹ [2026-08-30 05:36:30] Perform umap nonlinear dimension reduction
#> ✔ [2026-08-30 05:36:38] Standard processing workflow completed
pancreas_sub <- RunScrublet(pancreas_sub)
#> ℹ [2026-08-30 05:36:38] Running Scrublet
#> Error in if (existing_minor %in% c("3.10", "3.11", "3.12")) {    version <- paste0(existing_minor, "-1")}: argument is of length zero
CellDimPlot(
  pancreas_sub,
  reduction = "umap",
  group.by = "db.Scrublet_class"
)
#> Error in CellDimPlot(pancreas_sub, reduction = "umap", group.by = "db.Scrublet_class"): "db.Scrublet_class" is not in the meta.data of srt object

FeatureDimPlot(
  pancreas_sub,
  reduction = "umap",
  features = "db.Scrublet_score"
)
#> ! [2026-08-30 05:36:43] "db.Scrublet_score" are not in the features of <Seurat>
#> Warning: "db.Scrublet_score" are not in the features of <Seurat>
#> Error in FeatureDimPlot(pancreas_sub, reduction = "umap", features = "db.Scrublet_score"): There are no valid features present.