assessPuritySingle for MSMS from QTOF

[Marievlm]

Hi !

Thank you very much for your package. It is very useful to analyze MSMS spectra.

I would like to assess the purity of my MSMS data acquired on a QTOF and an Orbitrap for comparison. However, for QTOF data, I can't apply the function assessPuritySingle on an mzML file.

The error is the following :
Erreur dans if (scanids$pre == scn1) { : l'argument est de longueur nulle De plus : Message d'avis : Dans for (i in seq_len(n)) { : fermeture de la connexion inutilisée 11 (Data_001.mzML) (sorry it is in french).

I go to the traceback and here are presented the steps :
`8: linearPurity(rowi, scan_peaks, minoff, maxoff, ppm, scanids,
nearest, mostIntense, iwNorm, iwNormFun, ilim, plotP, plotdir,
isotopes, im)

7: .fun(piece, ...)

6: (function (i)
{
piece <- pieces[[i]]
if (.inform) {
res <- try(.fun(piece, ...))
if (inherits(res, "try-error")) {
piece <- paste(utils::capture.output(print(piece)),
collapse = "\n")
stop("with piece ", i, ": \n", piece, call. = FALSE)
}
}
else {
res <- .fun(piece, ...)
}
progress$step()
res
})(1L)
5: loop_apply(n, do.ply)
4: llply(.data = .data, .fun = .fun, ..., .progress = .progress,
.inform = .inform, .parallel = .parallel, .paropts = .paropts)
3: ldply(.data = pieces, .fun = .fun, ..., .progress = .progress,
.inform = .inform, .parallel = .parallel, .paropts = .paropts)
2: plyr::ddply(mrdfshrt, ~seqNum, .parallel = pBool, get_interp_purity,
scan_peaks = scans, ppm = ppmInterp, ms2 = mrdf[mrdf$msLevel ==
2, ]$seqNum, prec_scans = prec_scans, minoff = minoff,
maxoff = maxoff, mostIntense = mostIntense, plotP = plotP,
plotdir = plotdir, interpol = interpol, nearest = nearest,
iwNorm = iwNorm, iwNormFun = iwNormFun, ilim = ilim, isotopes = isotopes,
im = im)
1: assessPuritySingle(filepth = "Data_001.mzML")`

In advance, thank you for your reply,
Sincerely,

Marie