Compute the differential expression across each pair of cell types — differential_expression • tiltedCCA

Compute the differential expression across each pair of cell types

Usage

differential_expression(
  seurat_obj,
  assay,
  idents,
  slot = "data",
  test_use = "wilcox",
  verbose = T
)

Arguments

seurat_obj: seurat object
assay: name of assay in the seurat_obj
idents: variables name inside seuart_obj that contains the cell-type information (or clustering information) for each cell
slot: slot of seurat_obj[[assay]] that informs with data matrix will be used in the DE test
test_use: either "MAST" or "wilcox" dictates which DE test will be used
verbose: non-negative integer

Value

a list with elements "combn_mat", "de_list" and "level_vec"