Support overall survival data from gdc - Githubissues

stjude / proteinpaint

Data visualization and analysis framework focused on phenotype-molecular data integration at cohort level.

https://proteinpaint.stjude.org/

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Support overall survival data from gdc #1807

Closed xzhou82 closed 3 months ago

xzhou82 commented 3 months ago

Description

at gdc dictionary, Overall Survival is added as the first root term. some improvements to querySamples_gdcapi()

adding it to oncomatrix and gene exp clustering seems to work

it doesn't work for mds3 subtk filtering, same reason as unable to use gene exp for sample filtering for gdc (api issue)

Checklist

Check each task that has been performed or verified to be not applicable.

[ ] Tests: added and/or passed unit and integration tests, or N/A
[ ] Todos: commented or documented, or N/A
[ ] Notable Changes: updated release.txt, prefixed a commit message with "fix:" or "feat:", added to an internal tracking document, or N/A

xzhou82 commented 3 months ago

please test now. oncomatrix and mds3 tests pass. it remains to be seen if survival data query works for any gdc cohort filter.