Detect communication-dependent genes — communication_deg

Identify genes whose expression varies with communication intensity.

Usage

communication_deg_detection(
  seurat_obj,
  database_name,
  key = "total",
  signal_type = c("sender", "receiver"),
  assay = NULL,
  slot = "data",
  n_knots = 5L,
  genes = NULL,
  n_workers = 1L,
  verbose = TRUE
)

Arguments

seurat_obj: Seurat object with COMMOTR results.
database_name: Database name.
key: LR pair or pathway name (default: "total").
signal_type: "sender" or "receiver" communication.
assay: Assay to use.
slot: Expression slot.
n_knots: Number of spline knots for fitting (default: 5).
genes: Genes to test (default: NULL tests all variable genes).
n_workers: Number of parallel workers.
verbose: Print progress.

Value

Data frame with test statistics for each gene.

Details

Uses generalized additive models (GAM) to test for association between gene expression and communication intensity. P-values are adjusted using Benjamini-Hochberg method.