Update gene metadata file to remove biomart-only genes #132
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…nes. Also updates to Ensembl release 111.
|
jaclynbeck-sage
commented
Apr 26, 2024
| ) | ||
|
|
||
| df_filt = df.copy().loc[keep].reset_index(drop=True) | ||
| return df_filt | ||
|
|
||
|
|
||
| def r_query_biomart() -> pd.DataFrame: |
There was a problem hiding this comment.
This is code from the pre-processing notebook that I moved from the notebook to here as an unused function, instead of deleting it.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Changed the pre-processing notebook so it doesn't get all genes from Biomart anymore. It only gets info for genes that exist in our data sets. There are now only 37,452 genes in the metadata file. New gene metadata file is uploaded as version 13.