Hello,

I'm in need of some help with what I think is namespace administration. I'm
modifying some methods of the package PICS so that they can take GRanges
object (from the GenomicRanges package) as input.
In doing so, I want to use the method as.data.frame(GRanges) defined in the
GenomicRanges package.

But when I try to transform a GRanges object in a data.frame, I get this
error:
"Error in as.data.frame.default(gr, row.names = NULL, optional = FALSE) :
  cannot coerce class '"GRanges"' into a data.frame"

In the DESCRIPTION file of the package, I have included
    "Imports: ..., GenomicRanges, ..."

In the NAMESPACE file of the package, I have included:
     "importFrom(GenomicRanges)
     importClassesFrom(GenomicRanges, GRanges)
     importMethodsFrom(GenomicRanges, as.data.frame)"

If I do a showMethods("as.data.frame") from PICS namespace environment, I
get:
> showMethods(as.data.frame)
Function: as.data.frame (package base)
x="ANY"
x="AtomicList"
x="DataFrame"
x="DataFrameList"
x="GappedAlignments"
x="GappedRanges"
x="GenomicRanges"
x="GRangesList"
...

which shows that the "as.data.frame" method defined in GenomicRanges is
available (x="GRanges" is inherited from x="GenomicRanges"), but still, I
can't use as.data.frame on a GRanges object without getting this error:
"Error in as.data.frame.default(gr, row.names = NULL, optional = FALSE) :
  cannot coerce class '"GRanges"' into a data.frame"

Any idea what I am doing wrong?

Also, if anyone knows a good source of information on the syntax to use in
the NAMESPACE and DESCRIPTION files?

Thank you very much!

Frederic

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