Find differential markers using ClusterDE

Find differential markers using ClusterDE

Usage

findMarkers(
  obj,
  ident.1,
  ident.2,
  nCores = 1,
  nRep = 1,
  flavour = "classic",
  spatial = NULL
)

Arguments

obj

Seurat object containing expression data.

ident.1

Group identity to test as group 1.

ident.2

Group identity to test as group 2.

nCores

Number of CPU cores used for parallelization.

nRep

Number of null replicates.

flavour

Either "classic" or "pca"; selects null-construction method. classic: uses default count matrix as simulation input. pca: uses PCA approximation as simulation input, faster and more scalable when large number of replicates is needed.

spatial

A vector of 2 strings, the meta data column name representing X and Y coordinates if using spatial data. Default is NULL.

Value

A table of DEG results.

Examples

dummy_obj <- DUMMY
#> Error: object 'DUMMY' not found
findMarkers(dummy_obj, ident.1 = "cell_type_1", ident.2 = "cell_type_2")
#> Error: object 'dummy_obj' not found