Calculate Log2 Fold Change of In-Silico Perturbation

Computes the log2 fold change (Log2FC), mean delta, and average baseline expression for genes following an in-silico perturbation. It compares the perturbed assay against the baseline observed expression.

Usage

PerturbationLog2FC(
  seurat_obj,
  perturbation_name,
  assay_obs = "RNA",
  module = NULL,
  n_hubs = 10,
  pseudocount = 1,
  layer_norm = "data",
  layer_counts = "counts"
)

Arguments

seurat_obj: A Seurat object containing both the baseline and perturbed data.
perturbation_name: Character. The name of the assay containing the perturbed expression data.
assay_obs: Character. The name of the baseline assay. Default is 'RNA'.
module: Character. Optional. The specific hdWGCNA module name to analyze. If provided, the output will include a column indicating whether each gene is a top hub.
n_hubs: Integer. The number of top hub genes to flag if module is provided. Default is 10.
pseudocount: Numeric. Pseudocount added to average expression before log2 transformation to prevent infinite values. Default is 1.
layer_norm: Character. The layer/layer containing normalized data. Default is 'data'.
layer_counts: Character. The layer/layer containing raw counts. Default is 'counts'.

Value

A data.frame containing gene names, mean delta (raw counts difference), average baseline expression, Log2FC, and optionally module hub status.