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FindDifferentialRegulons

Source: R/Regulons.R
FindDifferentialRegulons.Rd

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

Value

A dataframe contaning differential regulon results

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.