[Bioc-devel] RFC: read.AnnotatedDataFrame

Martin Morgan mtmorgan at fhcrc.org
Thu May 24 15:36:49 CEST 2007

Wolfgang --

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).

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.


Wolfgang Huber <huber at ebi.ac.uk> writes:

> Dear all,
> I have a checked in a new function read.AnnotatedDataFrame2 into Biobase 
> (>= 1.15.12), which has (somewhat) different arguments from the existing 
> read.AnnotatedDataFrame:
> - different defaults for the  read.table options:
>     sep="\t", header=TRUE, quote ="", as.is=TRUE,
> - no 'widget' argument (which is anyway unimplemented).
> A nice feature is that the new function allows more easily to specify 
> the varMetadata.
> Ideally, I would like read.AnnotatedDataFrame2 to replace the existing 
> read.AnnotatedDataFrame, but for this would like to request your 
> feedback: is anyone very attached to the function 
> read.AnnotatedDataFrame in its current form? Would changing its API 
> break lots of things? Please speak up if "yes", otherwise I might 
> interpret that as "no".
> Best wishes
>    Wolfgang
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
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Martin Morgan
Bioconductor / Computational Biology

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