[BioC] Question about changes in package Ringo

[Seth Falcon]

"PT Bote" <ptbote86 at googlemail.com> writes:
> I have been using the package Ringo to analyze some ChIP-chip data
> some months ago
[snip]

> The peaks found back then all have a slot "modification" that stored
> on what kind of ChIP sample the peaks had been found. In this new
> version, the function "newPeak" and others do not mention such a
> slot anymore and it's not used by other functions any
> longer. Unfortunately I have used this slot in some of my own
> functions and these do not work anymore. I suspect is has been
> replaced by the slot "antibody", am I right?  Is there a simple way
> to update the "peak" objects?

I expect the Ringo maintainer will have some details for you...

I wanted to point out to anyone listening that any time you directly
use a slot in a class by using '@' you are very likely 
going _around_ the intended interface.  Many package authors use
classes and methods specifically to separate the implementation
details like slots and slot names from the user interface (the
methods).  The lesson?  If you find yourself using '@', ask yourself
if there is a way to get what you want without direct slot access.  If
not, send a question to the list and/or maintainer.

Hope that helps (or that it will help next time) :-)

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
BioC: http://bioconductor.org/
Blog: http://userprimary.net/user/