[Bioc-devel] RFC: read.AnnotatedDataFrame
Hi Martin,
There have been a couple of requests for widget support, so implementing rather than removing the widget option might be better (though of course more difficult -- there are several different paths through the code, users haven't been forthcoming about which are actually important to them, and different paths have different sets of bugs / design issues that make adoption to AnnotatedDataFrame more challenging than you might expect).
Frankly, if people can prepare a file easily with MS Excel and then call
is it a single file? the annotated data frame should have several components including pData, featureData, varMetadata? (apologies if i am misremembering the structure)
a simple function to read it into R, I do not see much of a use case for a widget. Anyway, I am not in a position to implement the widgets functionality, but if it turns out that someone is, maybe this would be something for the wonderful new Qt stuff rather than tcltk?
i think the widget approach is good for a multicomponent structure. particularly because it guides one through the components in case they don't retain them (as i don't). implementation in tcltk vs qt is not a big concern.
Currently, the outcome of using this option with read.AnnotatedDataFrame and read.AnnotatedDataFrame2 results in the same: an error. But we can keep it around in the function signature if it makes people happier :)
Along the same lines, the args to read.AnnotatedDataFrame were copied from read.phenoData; probably there are a number of scripts out there relying on these.
Hmm, but read.phenoData is a different function than read.AnnotatedDataFrame. Is your design goal that one should be able to simply replace all calls to read.phenoData in existing scripts with calls to read.AnnotatedDataFrame? I think people that move their scripts
that seems a reasonable step -- i think read.phenoData should be eliminated.