Exact p-value output file?

[ccl6]

Hi! I'm using the cellphonedb v5, Method2. But according to the results and description about the output file: "Pvalues fields: cell_a|cell_b: 1 if interaction is detected as significant, 0 if not." I only got binary 0 or 1 values in the statistical_analysis_pvalues.txt output file. But I couldn't find any files with exact pvalues. I'm wondering where I should find those exact p values from my output. Thanks!

I'm using the method2 according to the vignette:

from cellphonedb.src.core.methods import cpdb_statistical_analysis_method

cpdb_results = cpdb_statistical_analysis_method.call(
    cpdb_file_path = cpdb_file_path,                 # mandatory: CellphoneDB database zip file.
    meta_file_path = meta_file_path,                 # mandatory: tsv file defining barcodes to cell label.
    counts_file_path = counts_file_path,             # mandatory: normalized count matrix.
    counts_data = 'hgnc_symbol',                     # defines the gene annotation in counts matrix.
    active_tfs_file_path = active_tf_path,           # optional: defines cell types and their active TFs.
    microenvs_file_path = microenvs_file_path,       # optional (default: None): defines cells per microenvironment.
    score_interactions = True,                       # optional: whether to score interactions or not. 
    iterations = 1000,                               # denotes the number of shufflings performed in the analysis.
    threshold = 0.1,                                 # defines the min % of cells expressing a gene for this to be employed in the analysis.
    threads = 5,                                     # number of threads to use in the analysis.
    debug_seed = 42,                                 # debug randome seed. To disable >=0.
    result_precision = 3,                            # Sets the rounding for the mean values in significan_means.
    pvalue = 0.05,                                   # P-value threshold to employ for significance.
    subsampling = False,                             # To enable subsampling the data (geometri sketching).
    subsampling_log = False,                         # (mandatory) enable subsampling log1p for non log-transformed data inputs.
    subsampling_num_pc = 100,                        # Number of componets to subsample via geometric skectching (dafault: 100).
    subsampling_num_cells = 1000,                    # Number of cells to subsample (integer) (default: 1/3 of the dataset).
    separator = '|',                                 # Sets the string to employ to separate cells in the results dataframes "cellA|CellB".
    debug = False,                                   # Saves all intermediate tables employed during the analysis in pkl format.
    output_path = out_path,                          # Path to save results.
    output_suffix = None                             # Replaces the timestamp in the output files by a user defined string in the  (default: None).
    )

[datasome]

Hi ccl6,

statistical_analysispvalues*.txt file has the exact p-values - many thanks for pointing this out - the comment in https://github.com/ventolab/CellphoneDB/blob/master/notebooks/T1_Method2.ipynb was wrong and I have just corrected it. Good luck with your analysis with CellphoneDB and thank you again for your feedback.

Best,

Robert.