[Bioc-devel] BioC 2.5: Added scanDates slot to Biobase's eSetclass

Bengoechea Bartolomé Enrique (SIES 73) enrique.bengoechea at credit-suisse.com
Thu Jun 25 11:05:03 CEST 2009

Hi Henrik,

Although I work in a different field (finance), I completely agree that your proposal would be one of the most useful infrastructure additions to R. I saw your post on R-devel and completely aggreed with the suggestion (sad that nobody from R-base answered). It would maybe have important performance implications for standard arrays, so maybe a new class could be envisioned for it? I would volunteer to work in such a project, as I've been writting a lot of R code like that in the past.

For example, I've developed a class similar to AnnotatedDataFrame but based on S3 and with some pre-defined meta-information (prefix the type of each variable, user-defined coercion behaviour, allow/disallow NAs per variable, etc.) which will be soon submitted to CRAN, and experienced first-hand the need for this type of infrastructure.




Message: 1
Date: Thu, 18 Jun 2009 18:47:36 -0700
From: Henrik Bengtsson <hb at stat.berkeley.edu>
Subject: Re: [Bioc-devel] BioC 2.5: Added scanDates slot to Biobase's
To: "Kevin R. Coombes" <krcoombes at mdacc.tmc.edu>
Cc: bioC-devel <bioc-devel at stat.math.ethz.ch>,	Laurent Gautier
	<laurent at cbs.dtu.dk>
	<59d7961d0906181847y57c32463j7b39cb5aac2a978 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

To generalize this above the level of biology etc, some annotation data maps naturally *along the dimension* of arrays, not to each cell, e.g. rownames() and colnames() of a matrix.  One timestamp per array is such an attribute.  On June 7, 2009 I sent the message '[Rd]
Suggestion: Dimension-sensitive attributes' to R-devel;


to suggest to have a generic dimattr(<obj>, <name>) "getter" and "setter".  See example in that message.  Maybe such a design pattern helps here too?

Also, the MAGE people should already have spent a lot of time thinking and designing this kind of stuff.  Maybe something there?


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