Hi, On Wed, 2013-05-01 at 14:43 +0200, Thomas Dybdal Pedersen wrote: ... > I'm in the final stage of preparing an mzIdentML parser for submission > to Bioconductor (https://github.com/thomasp85/mzID) The parser is > intended to be quite sparse and not interpret the content of the > mzIdentML file that much.
That's great news to hear that PSI standards see more adoption in BioC. [...] > So the question is: How can I ensure that I extract the right value > from the spectrumID for an mzR compatible acquisitionNum? I realize > that the generation of the acquisitionNum in mzR is probably handled > by the RAMP module, but I hope some of the mzR folks (or others) can > help. RAMP is indeed the "problem" here. mzR has been developed with the concepts of pluggable backends in mind, and netCDF and RAMP are currently implemented. Please see https://github.com/sneumann/mzR/wiki/Extending-mzR for our ideas to add a "proper" pwiz backend, which directly wraps the pwiz msdata C++ object instead of indirectly going through RAMP. That new backend would solve your problems. Note also that Laurent Gatto also envisioned that the same approach could add a backend to mzIdentML. Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
