Extract analysis parameters and generate a methods text from a Seurat object

Reads the command history stored in seurat_object@commands to reconstruct the parameters used for normalization, variable feature selection, scaling, PCA, integration (Harmony / FastMNN / Seurat CCA), UMAP, and clustering. Returns both a structured summary list and a ready-to-paste methods paragraph.

Usage

ExtractMethods(seurat_object, cite_seurat = TRUE, modality = NULL)

Arguments

seurat_object

A Seurat object with commands recorded (i.e., the standard Seurat workflow functions were called directly on the object, not via custom wrappers that bypass command logging).

cite_seurat

Logical. Append a Seurat citation reminder at the end of the methods paragraph. Default TRUE.

modality

Character or NULL. Override the sequencing modality label used in the methods text. Typical values: "scRNA-seq", "snRNA-seq". NULL (default) auto-detects from seurat_object@misc$scSidekick_params or the "modality" metadata column.

Value

A named list with two elements:

summary

Named list of extracted parameter values.

methods_text

Character string - a draft methods paragraph ready to paste into a manuscript.