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Fix for updates in mzR: read centroiding information from files #325

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jorainer opened this issue Mar 23, 2018 · 3 comments
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Fix for updates in mzR: read centroiding information from files #325

jorainer opened this issue Mar 23, 2018 · 3 comments
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@jorainer

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@jorainer
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Fix for the changes in mzR that add column centroided to the data.frame returned by mzR::header (PR sneumann/mzR#153 in mzR).

Since there is also the parameter centroided. in readMSData I would suggest to use in the default case (i.e. centroided. = NA) the centroiding information reported in the mzML or mzXML, if centroided. = TRUE or FALSE it will overwrite the information read from the raw files.
@jorainer jorainer self-assigned this Mar 23, 2018
@lgatto
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lgatto commented Mar 23, 2018

Since there is also the parameter centroided. in readMSData I would suggest to use in the default case (i.e. centroided. = NA) the centroiding information reported in the mzML or mzXML, if centroided. = TRUE or FALSE it will overwrite the information read from the raw files.

Yes, excellent idea. There's already a isCentroidedFromFile function that might be useful.

@jorainer
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The changes in the sneumann/mzR#153 PR in mzR would make this function obsolete. mzR's pwiz module reads centroiding information directly from the file and returns it in the header (column "centroided").

jorainer added a commit that referenced this issue Mar 28, 2018
@jorainer
Issue #325: use centroided information from mzR::header
148e8aa 
- Use the centroided information reported by mzR::header in readMSData.
- Ensure that centroiding information is also provided to the writeMSData.
- Fix unit tests and update documentation.
@lgatto
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lgatto commented Apr 4, 2018

I suppose this can be closed too?

@lgatto lgatto closed this as completed Apr 4, 2018
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