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.