Chromatogram

[tobiasko]

Hi everyone,

are there any plans for an OO representation of chromatograms? My idea would be to derive Chromatogram objects from Spectra using an aggregation function and subsetting.

Example: TIC for all MS2 within 5-10 min of RT from Spectra instance S

all MS2 -> subset Spectra on MSlevel
within 5-10 min of RT -> subset Spectra on rtime
aggregation = sum(subset(S))

results in Chromatogram with intensity slot (time resolved intensity vector) plus meaningful metadata inherited from S and on how it was constructed (parameters used for construction)

What do you think?

[lgatto]

There is a Chromatograms package in the planning, that will be developed from what is currently available in MSnbase (1, 2) using similar design principles as we currently have in Spectra.

[lgatto]

See also here for broader plans.

[jorainer]

Just adding to @lgatto's answer: you can extract chromatographic data with the chromatogram method defined in MSnbase (and also xcms) packages - and this returns the above menationed objects. They should also support MRM/SRM data out of the box.

[tobiasko]

Cool. Thx for the updates.