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Convert Seurat Object to Single-Cell PhyloExpressionSet

Source: R/phyloset_sc.R
ScPhyloExpressionSet_from_seurat.Rd

Convert a Seurat object with phylostratum information into a ScPhyloExpressionSet object for single-cell phylotranscriptomic analysis. Automatically extracts dimensional reductions if present, or computes basic PCA and UMAP if none are available.

Usage

ScPhyloExpressionSet_from_seurat(
  seurat,
  strata,
  layer = "counts",
  selected_idents = NULL,
  name = "Single-Cell PhyloExpressionSet",
  seed = 42,
  ...
)

Arguments

seurat

A Seurat object containing single-cell expression data

strata

Factor vector of phylostratum assignments for each gene

layer

Character string specifying which layer to use from the Seurat object (default: "counts")

selected_idents

Character string specifying which metadata column to use for grouping (default: NULL, uses active idents)

name

A character string naming the dataset (default: "Single-Cell Phylo Expression Set")

seed

Integer seed for reproducible UMAP computation (default: 42)

...

Additional arguments passed to ScPhyloExpressionSet constructor

Value

A ScPhyloExpressionSet object

Examples

# Convert Seurat object to ScPhyloExpressionSet
# sc_set <- ScPhyloExpressionSet_from_seurat(seurat_obj, strata,
#                                           name = "Brain Development SC Dataset")