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Set Default Parameters for Network Extraction

set.defaults.Rd

This function updates or resets default settings used in downstream network extraction and analysis within a Seurat object. Defaults include pruning thresholds, response and predictor gene sets, co-expression measures, and transformation functions for effect estimates.

Usage

set.defaults(seurat.obj, clean.up = FALSE, defaults = list())

Arguments

seurat.obj

A Seurat object with a NNet.mod list stored in the misc slot. This list is created by run.nn.reg.

clean.up

A logical indicating whether to reset defaults to initial values (effect-based assay, quadratic transformation, self-loop removal, and pruning at cutoff 0.95). Default is FALSE.

defaults

A named list of default parameters to update. Valid entries include:

  • f A function mapping effect estimates to importance scores. Default is function(x) 2*x^2.

  • remove.self.loops Logical, whether to remove self-loops. Default: TRUE.

  • assay Co-expression measure to use for downstream analysis. Options: "effect", "p.val", or "meta.network".

  • predictors Character vector of predictor genes.

  • responses Character vector of response genes.

  • cutoff Numeric threshold for pruning, between 0 and 1. Default: 0.95.

Value

A Seurat object with updated default settings stored in misc$NNet.mod$defaults.

Details

The defaults list defines how networks are extracted and post-processed in downstream analyses (e.g., pruning, TF activity inference, meta-network learning). By setting clean.up = TRUE, all defaults are reset to standardized values. Only valid arguments present in the current NNet.mod$defaults are updated.

See also

run.nn.reg, prepare.reg

Examples

# Reset defaults to initial values
seurat.obj <- set.defaults(seurat.obj, clean.up = TRUE)
#> Error: object 'seurat.obj' not found

# Update only the cutoff threshold and assay
seurat.obj <- set.defaults(
  seurat.obj,
  defaults = list(cutoff = 0.5, assay = "p.val")
)
#> Error: object 'seurat.obj' not found

# Check updated defaults
Seurat::Misc(seurat.obj, "mod")$defaults
#> Error: object 'seurat.obj' not found