PerturbationTransitions — PerturbationTransitions • compact

This function computes cell-cell transition probabilities based on an in-silico perturbation experiment.

Usage

PerturbationTransitions(
  seurat_obj,
  perturbation_name,
  features,
  graph,
  use_velocyto = TRUE,
  use_graph_tp = FALSE,
  corr_sigma = 0.05,
  n_threads = 4,
  layer = "data",
  slot = "data",
  assay = "RNA"
)

Arguments

seurat_obj: A Seurat object
perturbation_name: A name for the in-silico perturbation that will be stored in the Seurat obejct
features: Selected features to use for the transition probability calculation
graph: Name of the cell-cell graph in the Graphs(seurat_obj)
corr_sigma: A numeric scaling factor for the correlation matrix.
n_threads: Number of threads for the correlation calculation
slot: Slot to extract data for aggregation. Default = 'data'
assay: Assay in seurat_obj containing expression information.

Value

A Seurat object with the cell-cell transition probabilities stored in the Graphs slot of the Seurat object.