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let's assume we have 9 samples containing only a cell type and this samples are divided into 3 groups -> healthy, mild, severe
and then I have to run the code which can find tutorial as follows:
bw_paths, bed_paths = export_pseudobulk(
input_data = cell_data,
variable = "VSN_cell_type",
sample_id_col = "VSN_sample_id",
chromsizes = chromsizes,
bed_path = os.path.join(out_dir, "consensus_peak_calling/pseudobulk_bed_files"),
bigwig_path = os.path.join(out_dir, "consensus_peak_calling/pseudobulk_bw_files"),
path_to_fragments = fragments_dict,
n_cpu = 10,
normalize_bigwig = True,
temp_dir = "/tmp",
split_pattern = "-"
)
The purpose is to find any differences between the groups.
Can I use group information in a variable option instead of cell information?
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