DEGS_scANANSE {AnanseSeurat}

DEGS_scANANSE

Description

Calculate the differential genes needed for ananse influence

Usage

DEGS_scANANSE(
  seurat_object,
  output_dir,
  min_cells = 50,
  cluster_id = "seurat_clusters",
  genome = "./scANANSE/data/hg38",
  RNA_count_assay = "RNA",
  additional_contrasts = "None"
)

Arguments

seurat_object

seurat object

output_dir

directory where the files are outputted

min_cells

minimum of cells a cluster needs to be exported

cluster_id

ID used for finding clusters of cells

genome

path to the genome folder used for the anansnake config file

RNA_count_assay

assay containing the RNA data

additional_contrasts

additional contrasts to add between clusters within cluster_ID

Value

None, outputs DEG files in the output directory

Examples

sce_small <- readRDS(system.file("extdata","sce_obj_tiny.Rds",package = 'AnanseSeurat'))
DEGS_scANANSE(sce_small, min_cells = 2, output_dir = tempdir())