Dear all,

I have been using the package Ringo to analyze some ChIP-chip data some
months ago using a custom algorithm for peak-finding but employing functions
from Ringo to generate "peak" objects and "peakList" objects. Now I have
updated Ringo to the current development version of the package (v1.1.15)
and wanted to have a fresh look on the data but came across a small problem.
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been replaced by the slot "antibody", am I right?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?

On another note,  the input function "readNimblegen" requires a file
similar to the provided example file example_files.txt that apparently
describes the used slides. I have created such a text file by typing it
myself, but it would be nice to have a way to generate such a file
automatically.

Cheers,
Pos

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