End-to-end GLEAM workflow
Usage
run_gleam(
object = NULL,
expr = NULL,
meta = NULL,
geneset = "hallmark",
geneset_source = "auto",
seurat = TRUE,
assay = NULL,
layer = NULL,
slot = NULL,
method = "ensemble",
group = NULL,
sample = NULL,
celltype = NULL,
comparison = c("group", "celltype", "within_celltype", "trajectory", "spatial"),
target_celltype = NULL,
level = "sample",
pseudotime = NULL,
lineage = NULL,
region = NULL,
backend = c("auto", "internal", "monocle3", "monocle", "slingshot"),
top_n = 20,
verbose = TRUE
)Arguments
- object
Seurat object.
- expr
Expression matrix for matrix mode.
- meta
Metadata for matrix mode.
- geneset
Geneset input.
- geneset_source
Geneset source.
- seurat
Input mode.
- assay
Seurat assay.
- layer
Seurat layer.
- slot
Legacy Seurat slot fallback.
- method
Scoring method.
- group
Group variable.
- sample
Sample variable.
- celltype
Celltype variable.
- comparison
Comparison mode.
- target_celltype
Target celltype for within-celltype comparison.
- level
Testing level.
- pseudotime
Pseudotime vector or metadata column name.
- lineage
Lineage vector or metadata column name.
- region
Spatial region/domain column name or vector.
- backend
Trajectory backend used when
comparison = 'trajectory'.- top_n
Number of top pathways.
- verbose
Print messages.