Mark FacileData::as.<BiocBox> functions as .Defunct()

[tomsing1]

Reproducible example:

library(FacileData)
fds <- exampleFacileDataSet()
as.DGEList(fds)  # works
as.SummarizedExperiment(fds)   # error:

Error in as.SummarizedExperiment.data.frame(x, covariates, feature_ids,  : 
  is.FacileDataSet(.fds) is not TRUE

[lianos]

Thanks for the report!

I'm not quite sure what's going south there, but these as.<sometihng> functions should be (will be) nuked and are currently replaced with biocbox(fds, "<something>")

So, you can do:

y <- biocbox(fds, "DGEList")
se <- biocbox(fds, "SummarizedExperiment")

... using the latest version from @main, of course :-)

Let me know if that works for you, and we can convert this issue to one that makes sure we .Defunct() all these as.<BiocBox> functions.

[tomsing1]

Yup biocbox works for this. Thank you for pointing it out!