Various bugs/suggestions about erminer HOT 4 CLOSED

1 is correct provided the geneSetDescription = "Latest_GO". User can set it to a local file and use that instead. Can have a function to do a 1 time download but it'll be merely download.file(goLink) Then user will have to provide a filepath. Currently they can do that by... download.file(goLink).

An alternative is to download on installation or on package load, maybe with a function to update at will, but this will make it hard to track which version you are using and will cause issues if the R package is installed to a place the user doesn't have write access.

2 Can I have the data and code you used in your attempts? scoreColumn can be changed to accept a number or a column name.

3, 4 Done. I can silence the download message as well.

5, 6 I am considering making wrapper functions instead of directing people to use this monolithic one that exposes everything. That way obscure options with sensible defaults can be pushed to the back without consequence.

7 is it this part of the output? Should we return it all?

multifunctionalityCorrelation=-0.0113
multifunctionalityEnrichment=0.4784
multifunctionalityEnrichmentPvalue=1.000
numAboveThreshold=9994

from erminer.

1: Many bioconductor annotation packages have a "cache" option which is true by default.
2. Making scoreColumn by name would be good. Test case en route.
5, 6: Yes, exactly.
7: I'll have to check but the main one I wanted among those was multifunctionalityCorrelation.

from erminer.

2 is done.
7 is done

That leaves the wrapper functions and deciding what to do with the go annotation file.

from erminer.

4 wrapper functions are out for the 4 tests.

from erminer.