The arguments used in the `/main/src/merge_xomics.py` file
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This file merges the omics data into a single matrix.

The default arguments for this script are as follows:

cmd = ' '.join(['python3', 'merge_xomics.py', 
      '--merge-distribution',
      #'--microarray-config-file', '"{}"'.format(microarray_config_file),  # Only used if using microarray data
      '--total-rnaseq-config-file', '"{}"'.format(trnaseq_config_file),
      '--mrnaseq-config-file', '"{}"'.format(mrnaseq_config_file),
      #'--scrnaseq-config-file', '"{}"'.format(scrnaseq_config_file),  # Only used if using scRNA-seq data
      '--proteomics-config-file', '"{}"'.format(proteomics_config_file),
      '--expression-requirement', '"{}"'.format(expression_requirement),
      '--requirement-adjust', '"{}"'.format(requirement_adjust),
      '--total-rnaseq-weight', '"{}"'.format(tweight),
      '--mrnaseq-weight', '"{}"'.format(mweight),
      #'--single-cell-rnaseq-weight', '"{}"'.format(scweight),  # Only used if using scRNA-seq data
      '--protein-weight', '"{}"'.format(pweight),
      '--no-hc'
               ])
!{cmd}

Arguments

Argument Required? Default Value Description
--merge-distribution No False Flag to merge zFPKM distributions.
Required if using iMAT reconstruction algorithm in create_context_specific_model.py.
Must have run rnaseq_gen.py with ‘zFPKM’ as --technique.
If --proteomics-config-file is given will merge proteomics distributions with
zFPKM distributions using a weighted scheme.
--microarray-config-file Yes False Name of microarray Excel configuration file found under /main/data/config_files/
--total-rnaseq-config-file No None The name of the total RNA-seq Excel configuration file found under /main/data/config_files/
--mrnaseq-config-file No None The name of the mRNA-seq Excel configuration file found under /main/data/config_files/
--scrnaseq-config-file No None The name of the single cell RNA-seq Excel configuration file found under /main/data/config_files/
--proteomics-config-file No None The name of the proteomics Excel configuration file found udner /main/data/config_files/
--expression-requirement No None Number of sources with active gene for it to be considered active even if it is not a high confidence-gene
--requirement-adjust No flat Technique to adjust expression requirement based on differences in number of provided data source types
--total-rnaseq-weight No 1 Total RNA-seq weight for merging zFPKM distribution
--mrnaseq-weight No 1 PolyA enriched (messenger) RNA-seq weight for merging zFPKM distribution
--single-cell-rnaseq-weight No 1 Single-cell RNA-seq weight for merging zFPKM distribution
--protein-weight No 2 Proteomics weight for merging z-score distribution
--no-hc No False Flag to prevent high-confidence genes forcing a gene to be used in final model irrespective of other other data sources