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export_pseudobulk about question #174

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sugiYag opened this issue Oct 9, 2024 · 0 comments
Open

export_pseudobulk about question #174

sugiYag opened this issue Oct 9, 2024 · 0 comments

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@sugiYag
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sugiYag commented Oct 9, 2024

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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