Run scPagwas/scPaGWAS

Run the optional scPagwas package from scop without bundling LD, pathway, or block-annotation resources. The wrapper validates required GWAS columns, normalizes output paths, and records provenance in Seurat tools or a result attribute.

Usage

RunscPagwas(
  srt = NULL,
  single_data = NULL,
  gwas_data,
  celltype_meta = NULL,
  block_annotation = c("hg38", "hg37", "custom"),
  output.dirs = tempdir(),
  cleanup_soar = TRUE,
  return_seurat = !is.null(srt) || inherits(single_data, "Seurat"),
  verbose = TRUE,
  ...
)

RunscPaGWAS(
  srt = NULL,
  single_data = NULL,
  gwas_data,
  celltype_meta = NULL,
  block_annotation = c("hg38", "hg37", "custom"),
  output.dirs = tempdir(),
  cleanup_soar = TRUE,
  return_seurat = !is.null(srt) || inherits(single_data, "Seurat"),
  verbose = TRUE,
  ...
)

Arguments

srt

Optional Seurat object used as single-cell input.

single_data

Optional Seurat object or path to an .rds file used by scPagwas.

gwas_data

GWAS summary statistics as a data frame.

celltype_meta

Optional Seurat metadata column used to set identities.

block_annotation

Genome build for bundled upstream annotations ("hg38" or "hg37") or a custom annotation path.

output.dirs

Output directory passed to scPagwas.

cleanup_soar

Deprecated compatibility argument. SOAR cleanup is managed by the upstream scPagwas backend and is ignored by scop.

return_seurat

Whether to return a Seurat object when one is available.

verbose

Whether to print the message. Default is TRUE.

...

Additional arguments passed to the upstream scPagwas function after filtering by its formal arguments.

Value

A Seurat object or upstream result list.