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Export a gene information table #23

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dhimmel opened this issue Sep 7, 2016 · 1 comment
Closed

Export a gene information table #23

dhimmel opened this issue Sep 7, 2016 · 1 comment
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@dhimmel
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dhimmel commented Sep 7, 2016 •
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Similar to how we have sample information in samples.tsv, it would be nice to create a table with gene information. The primary identifier is entrez_gene_id. Additional columns could be:

  • symbol
  • name
  • chromosome
  • n_mutations - number of mutated samples
  • median_expression - median gene expression
  • mad_expression - median absolute deviation of gene expression

I'm leaning towards a combined dataset for mutation and expression genes. But I could be convinced that splitting the datasets would be better.

We should probably get this information from entrez gene as @clairemcleod did in #12.

Labeling this issue a task awaiting a claimer.
@dhimmel dhimmel added the task label Sep 7, 2016
@cgreene
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cgreene commented Sep 8, 2016

@dhimmel median_expression and mad_expression explanations might need a quick edit.

@dhimmel dhimmel mentioned this issue Sep 27, 2016
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dhimmel added a commit to dhimmel/cancer-data that referenced this issue Oct 5, 2016
@dhimmel
Extract gene information
6497f35 
Closes cognoma#23
dhimmel added a commit to dhimmel/cancer-data that referenced this issue Oct 5, 2016
@dhimmel
Extract gene information
44b2502 
Closes cognoma#23
@dhimmel dhimmel mentioned this issue Oct 5, 2016
Closed
dhimmel added a commit to dhimmel/cancer-data that referenced this issue Oct 7, 2016
@dhimmel
Outsource Entrez Gene logic to cognoma/genes
5009e74 
`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 dhimmel mentioned this issue Oct 7, 2016
Merged
dhimmel added a commit that referenced this issue Oct 10, 2016
@dhimmel
Outsource Entrez Gene logic to cognoma/genes (#32)
781eff0 
* 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
dhimmel added a commit to dhimmel/cancer-data that referenced this issue Oct 10, 2016
@dhimmel
Extract gene information
b25c1b9 
Closes cognoma#23
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@cgreene @dhimmel