StampPerturbProvenance: record baseline provenance for a perturb assay

This function stores lightweight provenance metadata on a perturbation assay (e.g. created by ModulePerturbation()) indicating which baseline assay and layer(s) it was derived from.

Usage

StampPerturbProvenance(
  seurat_obj,
  perturb_assay,
  baseline_assay = "RNA",
  method = "ModulePerturbation",
  overwrite = TRUE
)

Arguments

seurat_obj: A Seurat object.
perturb_assay: Character; name of the perturbation assay to stamp.
baseline_assay: Character; baseline assay name used to generate the perturbation.
method: Character; description of how the assay was produced.
overwrite: Logical; overwrite existing provenance fields.

Value

Seurat object with provenance written to the assay misc.

Details

This enables CombinePerturbAssays() to perform a strict, deterministic check that all perturbation assays being combined were generated from the same baseline representation (e.g. baseline assay RNA vs SCT, and baseline layer counts).

Provenance is stored in seurat_obj[[perturb_assay]]@misc$COMPACT with fields:

baseline_assay
baseline_layers (e.g. "counts")
method
stamped_at