Run over-representation analysis for each stored CellRank trend module and keep complete tables and an execution manifest in the Seurat object.
Usage
RunCellRankEnrichment(
object,
lineage,
db = c("MSigDB_C2", "GO_BP", "GO_CC", "GO_MF", "MSigDB_H"),
species = "Mus_musculus",
universe = NULL,
minGSSize = 10L,
maxGSSize = 500L,
pvalue_cutoff = 0.05,
qvalue_cutoff = 0.2,
p_adjust_method = "BH",
show_category = 8L,
output_dir = NULL,
continue_on_error = FALSE,
verbose = TRUE,
srt = NULL
)Arguments
- object
A Seurat object returned by [RunCellRankTrends].
- lineage
CellRank lineage whose trend modules should be enriched.
- db
Annotation databases accepted by [PrepareDB].
- species
Species passed to [PrepareDB].
- universe
Background genes. `NULL` uses genes tested for CellRank lineage drivers.
- minGSSize
Minimum gene-set size.
- maxGSSize
Maximum gene-set size.
- pvalue_cutoff
Nominal enrichment cutoff.
- qvalue_cutoff
Adjusted enrichment cutoff.
- p_adjust_method
Multiple-testing method.
- show_category
Number of terms shown in each dot plot.
- output_dir
Optional directory for CSV/PDF exports.
- continue_on_error
Whether to keep other modules when one enrichment call fails. Failures are recorded in the manifest.
- verbose
Whether to print progress messages.
- srt
Deprecated alias for `object`; supply exactly one of the two. It will be removed in scop 1.0.0.
Value
The Seurat object with results under `object@tools$CellRank$enrichment[[lineage]]`. Each table in `databases` includes `Groups` and `Database` columns accepted by [EnrichmentPlot].