Run TradeSeq Differential Dynamics Analysis (Optimized for 2 Lineages)

Evaluates differential gene expression across exactly two developmental tubes. Employs aggressive proportional thresholding to drop uninformative genes, bypassing severe RAM and processing bottlenecks in tradeSeq.

Usage

mRunTradeSeqTocky(object, seurat_obj, ...)

# S4 method for class 'mCanonicalTockyObj'
mRunTradeSeqTocky(
  object,
  seurat_obj,
  tubes = NULL,
  min_pct = 0.05,
  n_knots = 5,
  n_cores = 1,
  p_adjust_method = "fdr"
)

Arguments

object

An mCanonicalTockyObj.

seurat_obj

The Seurat object to fetch counts from.

...

Additional arguments passed to methods.

tubes

Character vector of exactly two genes defining the tubes to compare (e.g., c("Cd4", "Cd8a")). If NULL, auto-detects if exactly two exist.

min_pct

Numeric. Minimum fraction of cells a gene must be expressed in (default 0.05, i.e., 5%).

n_knots

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

n_cores

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

p_adjust_method

Character. Correction method: "fdr" (default), "bonferroni", "holm", etc.