FindDifferentialRegulons: FindDifferentialRegulons

In smorabit/hdWGCNA: hdWGCNA

FindDifferentialRegulons

Description

Function to compare TF regulon scores between two sets of cell barcodes.

Usage

FindDifferentialRegulons(
  seurat_obj,
  barcodes1,
  barcodes2,
  assay = "RNA",
  slot = "data",
  layer = "data",
  wgcna_name = NULL,
  test.use = "wilcox",
  only.pos = FALSE,
  logfc.threshold = 0,
  min.pct = 0,
  verbose = FALSE,
  pseudocount.use = 0,
  ...
)

Arguments

seurat_obj	A Seurat object
barcodes1	character vector containing cell barcodes for the first group to test. Positive fold-change means up-regulated in this group.
barcodes2	character vector containing cell barcodes for the second group to test. Negative fold-change means up-regulated in this group.
assay	Assay to extract data for aggregation. Default = 'RNA'
slot	Slot to extract data for aggregation. Default = 'counts'. Slot is used with Seurat v4 instead of layer.
layer	Layer to extract data for aggregation. Default = 'counts'. Layer is used with Seurat v5 instead of slot.
wgcna_name	The name of the hdWGCNA experiment in the seurat_obj@misc slot
...	Additional parameters for the Seurat FindMarkers function

Details

FindDifferentialRegulons compares two groups based on their TF regulon scores. Three comparisons are made for different sets of features: positive regulon scores, negative regulon scores, and gene expression. The same settings for the test will be used for all three tests.

Value

A dataframe contaning differential regulon results

smorabit/hdWGCNA documentation built on Oct. 23, 2024, 11:19 p.m.