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lgatto / RforProteomics

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.
http://lgatto.github.io/RforProteomics
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msDataTab #12

Closed lgatto closed 8 years ago

lgatto commented 8 years ago

The MS data table currently looks like this.

Data type File format Data structure Package
Raw mzXML or mzML mzRpwiz or mzRramp mzR
Raw mzXML or mzML List of MassSpectrum objects MALDIquantForeign
Identification mzIdentML mzRident mzR
Identification mzIdentML mzID mzID
Quantitative mzTab MSnSet MSnbase
Raw mzXML or mzML MSnExp MSnbase
Peak lists mgf MSnExp MSnbase
Imaging imzML or Analyze 7.5 MSImageSet or list of MassSpectrum objects Cardinal or MALDIquantForeign

@sgibb could you split Cardinal and MALDIquantForeign on two different lines, as I have done for raw data, as the table becomes unnecessary wide like it is now (see the chapter for example).

sgibb commented 8 years ago

Done, now the table has the following format:

Data type File format Data structure Package
Raw mzXML or mzML mzRpwiz or mzRramp mzR
Raw mzXML or mzML list of MassSpectrum objects MALDIquantForeign
Identification mzIdentML mzRident mzR
Identification mzIdentML mzID mzID
Quantitative mzTab MSnSet MSnbase
Raw mzXML or mzML MSnExp MSnbase
Peak lists mgf MSnExp MSnbase
Imaging imzML or Analyze 7.5 MSImageSet Cardinal
Imaging imzML or Analyze 7.5 list of MassSpectrum objects MALDIquantForeign

@lgatto I would suggest to move the "Raw" row of MSnbase to the top. Then all "Raw" rows are grouped together. Or do you prefer to group by package?

lgatto commented 8 years ago

Thanks!

Data type File format Data structure Package
Raw mzXML or mzML mzRpwiz or mzRramp mzR
Raw mzXML or mzML list of MassSpectrum objects MALDIquantForeign
Raw mzXML or mzML MSnExp MSnbase
Identification mzIdentML mzRident mzR
Identification mzIdentML mzID mzID
Quantitative mzTab MSnSet MSnbase
Peak lists mgf MSnExp MSnbase
Imaging imzML or Analyze 7.5 MSImageSet Cardinal
Imaging imzML or Analyze 7.5 list of MassSpectrum objects MALDIquantForeign