search

cognoma / cancer-data

TCGA data acquisition and processing for Project Cognoma
Other
20 stars 28 forks source link

Process data into expression and mutation matrices #7

Closed dhimmel closed 8 years ago

cgreene commented 8 years ago

The 2.TCGA-process.ipynb notebook says "Notice that mutation type codes are not standardized. For example, 5_prime_UTR_variant, 5'UTR, UTR_5_PRIME all refer to the same type of mutation." but the corresponding table doesn't have these elements. Did this get cleaned up before the table is generated somehow?

clairemcleod commented 8 years ago

It seems like there is a bug with the exported .yml file and environment creation. execute.sh does not actually create an environment. It seems related to this conda issue.

dhimmel commented 8 years ago

Did this get cleaned up before the table is generated somehow?

@cgreene see https://github.com/cognoma/cancer-data/issues/2#issuecomment-233088248 -- the input data changed, resolving the issue. Will update the notebook.

cgreene commented 8 years ago

My comments have been addressed 👍

dhimmel commented 8 years ago

Cool @clairemcleod, would you like to merge if you think it's ready?

You'll want to use a "merge commit" rather than a "squash and merge" since there are multiple distinct commits. This is the default, but just wanted to clarify.