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UCLouvain-CBIO / depmap

Cancer Dependency Map package
https://uclouvain-cbio.github.io/depmap/
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depmap_mutationCalls() returning metadata table #64

Closed imkeller closed 3 years ago

imkeller commented 3 years ago

I am using the Bioconductor depmap package and I find it very useful and easy to use.

It seems like the depmap_mutationCalls() function is returning the metadata table. mutationCalls_19Q3() returns the correct mutation data. Could you take a look at it?

imkeller commented 3 years ago

Also, the ensembl_id in the table returned by depmap_TPM() looks like an entrez ID.

lgatto commented 3 years ago

Thank you for the issue, Katharina. Regarding

It seems like the depmap_mutationCalls() function is returning the metadata table. mutationCalls_19Q3() returns the correct mutation data.

there was indeed a bug where the copy numbers were returned instead of mutation calls, which should be fixed in GitHub, and soon on Bioconductor.

And indeed, the id isn't ensembl, but suspiciously looks like an entrez id. Will be fixed too.

lgatto commented 3 years ago

@tfkillian - I have fixed this in the script that generates the data. Could you update the data and update it on ExperimentHub, please.

lgatto commented 3 years ago

Pushed to Bioc, but waiting that the actual data is updated before closing the issue.

lgatto commented 3 years ago

@tfkillian - I have fixed this in the script that generates the data. Could you update the data and update it on ExperimentHub, please.

Has this been done? New release is planned today!

tfkillian commented 3 years ago

@lgatto This update will be pushed with the next data release.

tfkillian commented 3 years ago

All TPM datasets with Entrez ID have been updated and now are available on EH. @lgatto you can close this issue