number of common peaks in @matches

[stanstrup]

It would be nice to have the number of common peaks in @matches in addition to presence_ratio. When I take a quick look at matches I'd like to see if for example only a single peak was matched.

[jorainer]

Sure, makes sense.

[jorainer]

@stanstrup , can you check if you're happy with the recent changes and eventually close the issue?

[stanstrup]

It seems to always return 1...

fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML", package = "msdata")
pest_ms2 <- filterMsLevel(Spectra(fl), 2L)
pest_ms2 <- pest_ms2[c(808, 809, 945:955)]

load(system.file("extdata", "minimb.RData", package = "MetaboAnnotation"))

csp <- MatchForwardReverseParam(ppm = 10, requirePrecursor = FALSE, THRESHFUN = function(x)  which(x > 0)  )

mtches_test <- matchSpectra(pest_ms2, minimb, csp)

mtches_test@matches$matched_peaks_count %>% table

I also tested with my own larger set where this can definitely not be true and my own calculation (as per the docs compareSpectra(pest_ms2, minimb, FUN = function(x, y, ...) nrow(x), type = "inner", ppm = 10)) also don't get this.

[jorainer]

OMG, you're right @stanstrup ! Instead of adding the number of common peaks for one match I always replaced the whole column (see 4788bbc)! I'm really sorry for this terrible bug! Thanks for checking and reporting! It should be fixed now.

[stanstrup]

It is me that thanks you for bothering with my request. It works now. Thanks!