Cell Maps PPI Embedding

Description: {DESCRIPTION}

Version: {VERSION}

Usage

cellmaps_ppi_embeddingcmd.py [-h] --inputdir INPUTDIR [--dimensions DIMENSIONS] [--walk_length WALK_LENGTH] [--num_walks NUM_WALKS] [--workers WORKERS] [--p P] [--q Q] [--fake_embedder] [--provenance PROVENANCE] [--name NAME]
                                [--organization_name ORGANIZATION_NAME] [--project_name PROJECT_NAME] [--skip_logging] [--logconf LOGCONF] [--verbose] [--version]
                                outdir

Outputs

The tool creates several files and folders in the specified output directory.
Below is the list and description of each output generated by the tool.

Outputs
-------

- ppi_emd.tsv:
    A TSV file that contains the embeddings for the protein-protein interactions (PPIs). The first column consists of gene names, followed by the embedding vectors in subsequent columns.

            1	2	3	4
    HDAC2	0.00322267	0.068772331	0.087871492	0.074549779
    SMARCA4	0.014913903	-0.025018152	-0.01334604	-0.050020121
    DNMT3A	0.030166976	0.082494646	0.083659336	-0.005459526
    KDM6A	0.058055822	0.151974067	0.122265264	0.057505969
    RPS4X	0.016731756	0.046027087	0.041698962	0.010518731


Logs and Metadata
-----------------

- error.log:
    Contains error logs generated during the execution of the script.

- output.log:
    A log file detailing the standard messages, warnings, or any information generated during the execution.

- ro-crate-metadata.json:
    Metadata in RO-Crate format, a community effort to establish a lightweight approach to packaging research data with their metadata.
    The main object contains identifier (@id), type (@type), name, descriptions, keywords and isPartOf, that describes the hierarchical relationship (organization and project).
    Graph: The @graph key contains an array of objects that detail other entities related to the main dataset.
    a. Metadata, Datasets, Software
    b. Output Files: details of output files generated by the tool.
