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PNNL-CompBio / BeatAMLproteomics

Analysis of the 210 patient cohort processed by the OHSU/PNNL PTRC
MIT License
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Create file to download all beatAML data into memory #6

Closed sgosline closed 3 years ago

sgosline commented 3 years ago

To run the analysis that we did in the other repository we should create a single script that downloads all the data that we can source. An example of this file is here.

To date we only have proteomic, phosphoproteomic and clinical data in the following synapse tables, and should roughly map to the schemas generated by the loadBeatAMLData function in the pilot data:

  1. Proteomic: https://www.synapse.org/#!Synapse:syn25808020/tables/ image

  2. Phosphoproteomic: https://www.synapse.org/#!Synapse:syn25808662/tables/ (@mdnestor can you confirm that the ''corrected" data is batch corrected but NOT stoichiometry corrected)?

image

  1. Clinical/functional: https://www.synapse.org/#!Synapse:syn25830473/tables/ image
sgosline commented 3 years ago

solved by #9