myTAI (version 2.3.4)

ScPhyloExpressionSet_from_seurat: Convert Seurat Object to Single-Cell PhyloExpressionSet

Description

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,
  ...
)

Value

A ScPhyloExpressionSet object

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