Run GENIE3 regulatory network inference and return a standardized adjacency table with columns `TF`, `target`, and `importance`.
Usage
RunGENIE3(object, ...)
# S3 method for class 'Seurat'
RunGENIE3(
object,
assay = NULL,
layer = "counts",
regulators = NULL,
targets = NULL,
max_edges_per_target = Inf,
output_file = NULL,
cores = 1,
force = FALSE,
verbose = TRUE,
...
)
# S3 method for class 'matrix'
RunGENIE3(object, ...)
# Default S3 method
RunGENIE3(
object,
regulators = NULL,
targets = NULL,
genes_in = c("rows", "columns"),
max_edges_per_target = Inf,
output_file = NULL,
cores = 1,
force = FALSE,
verbose = TRUE,
...
)Arguments
- object
A Seurat object or expression matrix.
- ...
Additional backend-specific arguments.
- assay
Assay used when `object` is a Seurat object.
- layer
Assay layer used when `object` is a Seurat object.
- regulators
Candidate transcription factor genes.
- targets
Optional target genes. If `NULL`, all genes are considered.
- max_edges_per_target
Maximum incoming regulator edges retained per target. The default `Inf` keeps all positive-importance links.
- output_file
Optional path where the adjacency table is written.
- cores
Number of workers used by GENIE3.
- force
Whether to rebuild existing `output_file`.
- verbose
Whether to print progress messages.
- genes_in
Matrix orientation for matrix inputs. `"rows"` means genes x cells; `"columns"` means cells x genes.