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 [[alternative HTML version deleted]]

Hi Frederic, On 11-08-12 11:09 AM, Frederic Fournier wrote: > 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? Importing as.data.frame from IRanges seems to solve the problem. as.data.frame is implicitly turned into an S4 generic when IRanges is installed. Output of R CMD INSTALL IRanges: ... Creating a generic function for "as.data.frame" from package "base" in package ?IRanges? ... Cheers, H. > > 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319