Combine mpnst and mpnstpdx Datasets #425
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merging from origin
Sample file for 386 solid tumor PDX from the Novartis project.
…/coderdata into novartisPDX pulling from ruby's sample branch
Addition of drug data (~12 drugs were not matchable) and experiments from `calc_pdx_metrics.py`. `calc_pdx_metrics.py` was altered to skip auc calculations with fewer than 2 points (the linear model would not converge).
adding in improve sample and drug ids, added build_experiments.py, testing single experiments with linkml. More work to do with combo experiments.
Changes to calc_pdx_metrics.py include adding flexibility for `study` and `source` instead of being hard coded to MPNST. Added an if statement around the final touches to combos dataset, because if there is no drug data for the combo drugs, errors arise. Moved writing combos to csv to be inside this if statement.
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Check the pdx script from novartis-pdx-drugs-experiment branch. |
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Just a note, I'm receiving some errors with the latest PDX version. Working on resolving. |
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novartis update for PDX is working, error was on my side. This is ready to be reviewed (and merged) |
sgosline
approved these changes
Jul 25, 2025
build/build_all.py
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| @@ -40,7 +40,7 @@ def main(): | |||
| parser.add_argument('--figshare', action='store_true', help="Upload all local data to Figshare. FIGSHARE_TOKEN must be set in local environment.") | |||
| parser.add_argument('--all',dest='all',default=False,action='store_true', help="Run all data build commands. This includes docker, samples, omics, drugs, exp arguments. This does not run the validate or figshare commands") | |||
| parser.add_argument('--high_mem',dest='high_mem',default=False,action='store_true',help = "If you have 32 or more CPUs, this option is recommended. It will run many code portions in parallel. If you don't have enough memory, this will cause a run failure.") | |||
| parser.add_argument('--dataset',dest='datasets',default='broad_sanger,hcmi,beataml,cptac,mpnst,mpnstpdx,pancpdo,bladderpdo,sarcpdo,liverpdo',help='Datasets to process. Defaults to all available.') | |||
| parser.add_argument('--dataset',dest='datasets',default='broad_sanger,hcmi,beataml,cptac,pancpdo,bladderpdo,sarcpdo,liverpdo,mpnst',help='Datasets to process. Defaults to all available.') | |||
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Can we remove cptac from this?
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Removed cptac and merging |
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This merges the mpnst and mpnstpdx datasets with a single set of scripts.
This address issues #258, #356, #400, #423.