Non-unique identifiers for ions

[melpetera]

Sometimes there are redundant ion identifiers, especially when using RT in minutes (for example "M123.32T11" for two different ions with mass 123.32 and RT 10.6 min and 11.4 min).

Since identifiers are meant to be unique, something must be done (currently users add more decimal places for mass, change RT in seconds and/or modify identifiers themselves).

[lecorguille]

Are we agree that it's important during the peaklist export (currently camera.annotate, camera.combinexannot and soon xcms.fillpeaks) ?

If so, do you want that those redundant ion identifiers to be spotted and corrected automatically by increasing the number of digit?

[lecorguille]

Crossref: https://github.com/workflow4metabolomics/camera/issues/11

[lecorguille]

Done for FillPeaks-2.0.8: https://github.com/workflow4metabolomics/xcms/blob/bfb80b96ab0497a8d1fd853b779a26897f765929/galaxy/xcms_fillpeaks/abims_xcms_fillPeaks.xml#L45

[yguitton]

just a note they're is a function called xcmss:::groupnames in xcms that can be used (with function(xcmsSet object, mzdec = 0, rtdec = 0, template = NULL) with that even if a duplicate name is found it will be converted to MxTy_z

[lecorguille]

@yguitton Good suggestion but ... how do you use groupnames

I try without template

ids <- groupnames(xset, mzdec = numDigitsMZ, rtdec = numDigitsRT, template = NULL)

but:

|  Error in strsplit(template[1], "[T_]") : non-character argument
|  Calls: getPeaklistW4M -> groupnames -> groupnames -> .local -> strsplit

Help is welcome because they isn't so much documentation 👎

[lecorguille]

@melpetera Is make.unique is enough? here

ids <- make.unique(paste0("M",round(groups[,1],numDigitsMZ),"T",round(groups[,4],numDigitsRT)))

[lecorguille]

@melpetera @yguitton UP!

[melpetera]

About make.unique: I would add the sep="_" argument because identifiers already have points in it. But I think this can do!

[lecorguille]

From xcms.group 2.1.1 and xcms.fillpeaks 2.1.1 as discussed here: https://github.com/workflow4metabolomics/xcms/issues/36

[lecorguille]

docker run -d -p 8080:80 quay.io/workflow4metabolomics/galaxy-workflow4metabolomics:beta

[lecorguille]

Available within the dev galaxy instance

[melpetera]

Tested on dev galaxy instance! It is ok for me.

[lecorguille]

• [X] validated by @melpetera
• [x] validated by @yguitton
• [ ] validated by @jfrancoismartin

[lecorguille]

Validated