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UCLouvain-CBIO / depmap

Cancer Dependency Map package
https://uclouvain-cbio.github.io/depmap/
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depmap_copyNumber() function does not return CN data; returns metadata table #83

Closed mfper closed 1 year ago

mfper commented 1 year ago

Hi,

I just wanted to bring this to your attention; in the vignette it says:

The most recent copyNumber dataset can be automatically loaded into R by using the depmap_copyNumber function.

But it just returns a metadata table. The output is formaly identical to depmap_metadata.

This can even be seen in the vignette output for depmap_copyNumber()

Thanks a lot for the very useful package,

MFP

tfkillian commented 1 year ago

@mfper, the depmap_copyNumber function is working fine for me, so I can't replicate this error. Can you let me know what version of R and Bioconductor you are using? I suggest updating R to the latest dev version. If this fails to resolve the error, please use the following code to access the most recent version of the copyNumber dataset:

eh <- ExperimentHub::ExperimentHub(); AnnotationHub::query(eh, "depmap"); copyNumber <- eh[["EH7555"]]

mfper commented 1 year ago

Hi tfkillian,

Following the vignette I had previously manageed to get the CNs with the code that you pasted in your reply.

In fact, now when I try it, depmap_copyNumber() works.

I recently updated to R v4.2.2 so I suppose that's why.

Unfortunately I am not sure which version I was using before the update.

Kind regards,

MFP