Various Data fixes and Schema Alignments needed.

[jjacobson95]

This may not be up to date as I'm using some of the synapse data generated last week but I'm just trying to get ahead of a few fixes.

• BeatAML mutations file has a column titled "mutations" instead of "mutation". This should already be fixed in main, but I noticed it was wrong in those files.

• DepMap proteomics has the index column in it. just add 'index=False' argument to pd.to_csv.

• DepMap Experiments file dose_reponse_metrics have these values: fit auc', 'fit ic50', 'fit ec50', 'fit r2', 'fit ec50se', 'fit einf'.

  • All spaces should be replaced by underscores (example: "fit auc" changed to "fit_auc"). Originally the schema had spaces in it, but this was a mistake as the spaces were invalid and causing issues.

• DepMap experiments file has these extra columns:

[jjacobson95]

I'll note other issues as I find them in this thread.

Schema alignments - all of the following must be converted from float to integer:

• improve_sample_id in depmap_experiments
• entrez_id in depmap_proteomics
• entrez_id in depmap_transcriptomics
• entrez_id and improve_sample_id in depmap_mutations
• entrez_id in depmap_copy_number
• improve_sample_id in beataml_experiments

Never mind on these - I think this is just how pandas is reading them into the dataframes.

[sgosline]

I'm guessing these were all a result of my working off of main instead of the builder branch that was way ahead, I'll get to these shortly, still fixing another docker build issue.

[jjacobson95]

Okay taking a look at the new build (2024_03_20 build) and here are a couple updates needed to get these aligned to the schema and working with the package:

• mpnst mutations file: 'mutations' column should be named 'mutation'.
• beataml mutations file: 'mutations' column should be named 'mutation'. (This is fixed on main, just confirmed again.)
• beataml sampes file: model type has 'ex vivo' instead of 'tumor'. (This is also fixed on main) (also missing drugs, experiments files in this version as you mentioned you are working on)

[jjacobson95]

Another issue with the 2024_03_20 build that I just found: Depmap proteomics file is missing most of its data. There is only proteomics info for a single sample.

[sgosline]

please create separate issues so i can tag them. this was an easy fix, and is going in the latest PR.

[sgosline]

110 fixes these