Canonical Redundancy Analysis for Tocky Differentiation

Usage

mCanonicalTockySeq(
  object,
  temporal_col,
  b_ident = "B",
  br_ident = "BR",
  r_ident = "R",
  lineage_col,
  lineage_idents,
  lineage_names = NULL,
  top_n = 100,
  custom_genes = NULL,
  layer = "data",
  scale_Z = TRUE
)

Arguments

object: A Seurat object.
temporal_col: Character. Metadata column for temporal anchors.
b_ident: Character. Identity for the Blue (New) landmark (default "B").
br_ident: Character. Identity for the Blue-Red (Persistent) landmark (default "BR").
r_ident: Character. Identity for the Red (Arrested) landmark (default "R").
lineage_col: Character. Metadata column for lineage endpoints.
lineage_idents: Character vector of identities in Seurat object for lineage endpoints.
lineage_names: Optional character vector. Biological names for the lineages (e.g., c("CD4", "CD8")).
top_n: Integer. Number of marker genes to extract per group (default 100).
custom_genes: Optional character vector to skip marker calculation.
layer: Character. The Seurat layer to use (default "data").
scale_Z: Logical. Whether to scale the Z matrix (default TRUE).

Value

An object of class mCanonicalTockyObj.