The arguments used in the `/main/src/proteomics_gen.py` file
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This file creates proteomics matrices for downloaded proteomics data.
The default command for this block is as follows:
cmd = ' '.join(['python3', 'proteomics_gen.py',
'--config-file', '"{}"'.format(proteomics_config_file),
'--replicate-ratio', '"{}"'.format(rep_ratio),
'--high-replicate-ratio', '"{}"'.format(high_rep_ratio),
'--batch-ratio', '"{}"'.format(batch_ratio),
'--high-batch-ratio', '"{}"'.format(high_batch_ratio),
'--quantile', '"{}"'.format(quantile)])
| Argument | Required? | Default Value | Description |
|---|---|---|---|
--config-file |
Yes | The configuration file name to use | |
--replicate-ratio |
Yes | The ratio of replicates required for a gene to be considered active in that sample | |
--high-replicate-ratio |
Yes | The ratio of replicates to be considered “high confidence”. High confidence genes are considered expressed no matter what other data sources say |
|
--batch-ratio |
Yes | The ratio of batches required for a gene to be considered active in that sample | |
--high-batch-ratio |
Yes | The ratio of batches to be considered “high confidence”. High confidence genes are considered expressed no matter what other data sources say |
|
--quantile |
Yes | The percentage to be considered for each quantile |