[BioC] Question about changes in package Ringo

[Joern Toedling]

Dear Pos,

hello again. You are right, in the development version, the element name
"modification" has been renamed to "antibody", since I think this term
is more general and eventually it's the chosen antibody that defines
which genomic regions are enriched in the ChIP. I am sorry that this
change interfered with your functions. I have changed all relevant
functions in Ringo accordingly to avoid any problems with this renaming,
but of course the renaming could have created problems with user-created
functions. I will try to make such changes more transparent. In the end,
I would be happy to make the class "peak" for ChIP-enriched regions as
accessible as possible for ChIP-chip users in general. And even though I
find S4 classes a bit too tedious, maybe I should replace the current S3
class by a less break-prone S4 one soon. (And I know that the name
"peak" is a bit unfortunate too since it rather describes a genomic
stretch that seems to have been enriched in the ChIP. The probe-level
signal in that region, however, may show one or more  actual peaks or
just a long elevated plateau.) For the moment, I am afraid, you have to
do a manual update of the "peak" objects. Say "pl" is your list of peak
objects, then something like
pl <- lapply(pl, function(p) {p$antibody=p$modification;
p$modification=Null; return(p)})
may work for you. Please let me know if it does not.

> 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.
>   

Thank you for the suggestion. Another user had already mentioned that
the file "SampleKey.txt" that NimbleGen sends with the pair files could
be used for this. In the development version, the scripts directory
contains a script "convertSampleKeyTxt.R" which may give some ideas how
to generate a targets file from it.

Best regards,
Joern