Create a SpaMTP Seurat Object containing expression values for all present pathways

This function computes pathway-level scores from analyte-level expression data and stores the results as a new assay in a Seurat object. Each pathway score is calculated as the scaled mean expression of the analytes associated with that pathway, adjusted by the square root of the pathway size.

Usage

CreatePathwayObject(
  object,
  assay = SeuratObject::DefaultAssay(object),
  slot = "scale.data",
  new.assay = "pathway",
  remove.nans = TRUE,
  database = NULL,
  database_version = "latest",
  database_source = c("auto", "bundled", "local"),
  database_local_dir = NULL
)

Arguments

object: A SpaMTP Seurat object containing the expression data.
assay: Character. Name of the assay to extract analyte expression from. If no value is assigned, the DefaultAssay of the SpaMTP Seurat Object will be used (default = DefaultAssay(object)).
slot: Character. Which data slot to use (e.g., "scale.data") (default = "scale.data").
new.assay: Character. Name of the new assay where pathway scores will be stored (defaults = "pathway").
remove.nans: Logical. Whether to remove pathways with all NaN values (e.g., no matched analytes) (defaults = TRUE).
database: Optional named list of database resources, normally created by LoadSpaMTPDatabase().
database_version: Database snapshot version used for pathway lookup.
database_source: Database source; see LoadSpaMTPDatabase().
database_local_dir: Optional local RDS resource directory.

Value

A SpaMTP Seurat object with a new assay containing pathway-level expression scores. Feature names are adjusted to use underscores instead of dashes.

Examples

utils::str(formals(CreatePathwayObject))
#> Dotted pair list of 9
#>  $ object            : symbol 
#>  $ assay             : language SeuratObject::DefaultAssay(object)
#>  $ slot              : chr "scale.data"
#>  $ new.assay         : chr "pathway"
#>  $ remove.nans       : logi TRUE
#>  $ database          : NULL
#>  $ database_version  : chr "latest"
#>  $ database_source   : language c("auto", "bundled", "local")
#>  $ database_local_dir: NULL
#object <- CreatePathwayObject(seurat_obj, assay = "RNA", slot = "scale.data")