Refactoring Pancancer Ras Analysis #82
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adding R packages update R environment
convert to pdf from svg remove checkpoint call
also correct flags
better comments and flow control swap steps 7 and 8 update data path as well one line per command
update to pdf and convert to AUPR create figures folder
| @@ -43,8 +43,6 @@ | |||
| default: False if flag omitted | |||
| --x_matrix string of which feature matrix to use | |||
| default: raw | |||
| --y_matrix string of which status matrix to use | |||
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so y_matrix is always pancan_mutation_freeze? any reason for it?
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pancan_mutation_freeze is a large sample by gene matrix indicating mutation status for all of TCGA. Previously, the functionality included using the data provided by xena. At the time, xena was open source TCGA, but the PanCanAtlas was embargoed (updated data, mutation calls, etc.). Now that TCGA is public, we will only provide the options to use this updated data.
In the future, it would be nice to allow updates to this matrix (i.e. a different way to define positive samples). For the sake of this PR being for refactoring, I will wait to introduce this feature in a new PR.
README.md
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| | `--x_matrix` | `raw` | if not "raw", then the filename storing the features | | ||
| | `--y_matrix` | `default` | can also be "xena" | |
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| # Ensure that the path is starting in the scripts directory | ||
| if not cwd.split('/')[-1] == 'scripts': | ||
| os.chdir(os.path.join(cwd, 'scripts')) |
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this file is in the scripts folder already
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ah. I was picturing that someone may use these scripts without your directory structure in place
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i think the error message that would occur in this scenario is sufficient.
This is the first step referencing #77 - included in this PR are several, mostly minor, updates to the pancancer Ras analysis pipeline. Most of the changes are style updates. The next PR will include the actual files that are generated from a call to
bash analysis.sh.