Extract gene information #30
Closed
Conversation
This file contains hidden or 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
Member
Author
|
Here's the head of
|
entrez_gene_id was a float due to odd behavior by df.merge in pandas. This resulting in `float_format='%.4g'` of to_csv causing exponent formatting of entrez_gene_id and irreversibly corrupting their IDs.
Member
Author
|
Do not review yet --- will update in the wake of cognoma/genes#1. |
dhimmel
added a commit
to dhimmel/cancer-data
that referenced
this pull request
Oct 7, 2016
`0.genes-download.ipynb` is a notebook to download datasets from `cognoma/genes`. Update `2.TCGA-process.ipynb` to use the gene mapping guidelines in cognoma/genes#1. Remove `mapping/PANCAN-mutation/` since this mapping is now done in `2.TCGA-process.ipynb`. Closes cognoma#23. Closes cognoma#30 by exporting gene info files in `2.TCGA-process.ipynb`
dhimmel
added a commit
that referenced
this pull request
Oct 10, 2016
* Outsource Entrez Gene logic to cognoma/genes `0.genes-download.ipynb` is a notebook to download datasets from `cognoma/genes`. Update `2.TCGA-process.ipynb` to use the gene mapping guidelines in cognoma/genes#1. Remove `mapping/PANCAN-mutation/` since this mapping is now done in `2.TCGA-process.ipynb`. Closes #23. Closes #30 by exporting gene info files in `2.TCGA-process.ipynb` * Average expression values for the same gene * Update cognoma/genes download location
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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Outdated suggestions cannot be applied.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.
Closes #23
This downloads the latest Entrez Gene information from their FTP site (updated daily). Obsoleted genes have missing values for the columns from Entrez Gene. Unclear how we want to proceed wrt making the backing/django-genes and cancer-data use the same gene data.