export_ATAC_maelstrom {AnanseSeurat}

export_seurat_Maelstrom

Description

normalize and export the peak table of a seurat object based on clusters

Usage

export_ATAC_maelstrom(
  seurat_object,
  output_dir,
  min_cells = 50,
  ATAC_peak_assay = "peaks",
  cluster_id = "seurat_clusters",
  select_top_rows = TRUE,
  n_top_rows = 1e+05
)

Arguments

seurat_object

object

output_dir

directory where the files are outputted

min_cells

minimum of cells a cluster needs to be exported

ATAC_peak_assay

assay of the seurat object containing the peaks and peakcounts

cluster_id

ID used for finding clusters of cells

select_top_rows

only output the top variable rows, or all rows if false

n_top_rows

amount of variable rows to export

Value

None, outputs maelstrom peak counts table in the output directory

Examples

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