IPO tool: recommended changes and feature requests

[andzajan]

• IPO for xcmsSet

  • centWave peak picking algorithm needs option to optimise following parameters together:
    peakpickingParameters$min_peakwidth (Range for Min peak width range in seconds)
    peakpickingParameters$max_peakwidth (Range for Max peak width range in seconds)
    peakpickingParameters$ppm (Range for tolerated ppm m/z deviation in consecutive scans in ppm)
    peakpickingParameters$mzdiff (Range for Minimum difference in m/z for peaks with overlapping Retention Times)

• IPO for group and retcor

  • For grouping method denstiy allow to optimise range of bw and mzwid simultaneously
    retcorGroupParameters$bw (*Range for Bandwidth)
    retcorGroupParameters$mzwid (*Range for width of overlapping m/z slices)

[lecorguille]

Should be available with this commit: 5a5e663

[andzajan]

Thank you @lecorguille, I think there is a problem with parameters input interface now:

• would be possible for grouping parameter to make that if input is a single value and not a range, to keep that parameter fixed and optimise only other one;
• for retention time correction method obiwarp parameters are listed as non-optimisable, but m/z step input still has to be range.