Match Single-Cell Expression Data with Phylostratum Map (Seurat)

Join single-cell gene expression data (from a Seurat object) with a phylostratum mapping to create a ScPhyloExpressionSet object. Automatically extracts dimensional reductions and metadata.

Usage

match_map_sc_seurat(
  seurat,
  phylomap,
  layer = "counts",
  strata_legend = NULL,
  ...
)

Arguments

seurat

A Seurat object containing single-cell expression data

phylomap

A data frame with two columns: phylostratum assignments and gene IDs

layer

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

strata_legend

A data frame with two columns: phylostratum assignments and name of each stratum. If NULL, numeric labels will be used (default: NULL)

...

Additional arguments passed to ScPhyloExpressionSet_from_seurat

Value

A ScPhyloExpressionSet object

Details

This is a convenience function that combines phylostratum mapping with Seurat object conversion. Only genes present in both the expression data and phylomap will be retained. The function extracts all metadata and dimensional reductions from the Seurat object.

Examples

if (FALSE) { # \dontrun{
# Match Seurat object with phylostratum map
sc_set <- match_map_sc_seurat(seurat_obj, phylo_map, layer = "counts")
} # }