config_scANANSE {AnanseSeurat} | R Documentation |
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())
[Package AnanseSeurat version 1.2.0 Index]