Run TradeSeq Differential Dynamics Analysis on Tocky Trajectory

A wrapper function to perform differential dynamic expression testing using tradeSeq. Supports Seurat v5+ (uses 'layer') and matrix inputs.

Usage

RunTradeSeqTocky(
  object,
  gradient_res,
  group_by,
  genes,
  n_knots = 5,
  n_cores = 1
)

Arguments

object

A Seurat object OR a sparse expression matrix (Genes x Cells).

gradient_res

The data frame returned by GradientTocky_Slerp (must contain $angle).

group_by

If object is Seurat: Character string of the metadata column name (e.g., "treatment"). If object is Matrix: A named factor/character vector of groups matching column names.

genes

Character vector of genes to test (e.g., output of SelectTockyGenes).

n_knots

Integer. Number of knots for the GAM (default 5).

n_cores

Integer. Number of cores for parallel processing (default 1).

Value

A list containing:

results

Data frame of differential dynamics results (p-values, FDR).

gam_fit

The raw tradeSeq GAM object (for downstream plotting).