config_scANANSE {AnanseSeurat}

config_scANANSE

Description

This functions generates a sample file and config file for running Anansnake based on the seurat object

Usage

config_scANANSE(
  seurat_object,
  output_dir,
  min_cells = 50,
  cluster_id = "seurat_clusters",
  genome = "./scANANSE/data/hg38",
  additional_contrasts = c()
)

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

genomepy name or location of the genome fastq file

additional_contrasts

additional contrasts to add between clusters within cluster_ID

Value

None, outputs snakemake config file 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())