Changing column names of chromatogram data.frames

[philouail]

Hi,

Would it be possible to have the chromatogram() data.frames column names changed to "rtime" and "intensity" ? instead of "time" and their respective IDs

Currently implementing a mzR backend in Chromatograms and this change would really help efficiency so i would not need to loop through all the data.frames in the list only to change the colnames. These names are also in xcms (rtime()/intensity()) and Spectra (spectraVariables) so it would be better for consistency.

> MRM_file <- system.file("proteomics", "MRM-standmix-5.mzML.gz", package = "msdata")
> chromFile <- mzR::openMSfile(MRM_file)
> chromatogram(chromFile, 1) |> head()
          time      TIC
1 1.666667e-05 45.37833
2 4.233333e-03 44.39301
3 8.450000e-03 45.33704
4 1.266667e-02 44.30909
5 1.686667e-02 45.40231
6 2.108333e-02 44.29813
> chromFile <- mzR::openMSfile(MRM_file)
> chromatogram(chromFile, 2) |> head()
      time X..SRM.SIC.Q1.89.Q3.40.996.start.5.21145.end.15.20321667
1 5.211450                                                 42.34048
2 5.220850                                                 41.97664
3 5.230250                                                 41.46709
4 5.239650                                                 41.26899
5 5.249033                                                 41.12252
6 5.258433                                                 41.24522

[lgatto]

I think this would be a good change, to align the headings with the spectra data.

[sneumann]

Would we know any users for which this would be a breaking change ? Yours, Steffen

[jorainer]

it would break a unit test of Nils @nilshoffmann :) - apart from that, the only place that I know uses the chromatogram functionality from mzR is MSnbase. and there we are ignoring the column names: https://github.com/lgatto/MSnbase/blob/master/R/readChromData.R#L145-L150