bin_Spectra bug

[mtrnka]

Hi all,
First of all, thanks for this project. I'm working on some spectral library matching and have found all the RforProteomics libraries very useful.

I found a bug in functions-Spectrum.R. The function bin_Spectra calculates the breaks from the combined range of the two spectra objects. It then passes the breaks to function bin_Spectrum. bin_Spectrum contains an if clause that checks that the mz range of the spectrum actually falls within breaks and if not extends the breaks. The way it is coded it applies this only to the spectrum that exceeds the range leaving the other spectrum with the original range.

This is causing problems for me as I am trying to extract out peaks based on dot-product matching to reference spectra against an entire mzML file and inevitably cases crop up where it is trying to calculate dotproducts on nonconformable matrices because of the difference in bin-sizes.

I've fixed this issue for myself as noted below, but wanted to give you guys a heads up.

bin_Spectra <- function(object1, object2, binSize = 1L,
                        breaks = seq(floor(min(c(mz(object1), mz(object2)))),
                                     ceiling(max(c(mz(object1), mz(object2))))+binSize,
                                     by = binSize)) {
    return(list(bin_Spectrum(object1, binSize = binSize, breaks = breaks),
                bin_Spectrum(object2, binSize = binSize, breaks = breaks)))
}

[sgibb]

Thanks for reporting this! The bug was introduced while fixing #137. Here is an MWE:

s1 <- new("Spectrum2", mz=1:4, intensity=1:4)
s2 <- new("Spectrum2", mz=1:5, intensity=1:5)

lapply(MSnbase:::bin_Spectra(s1, s2), 
       function(x)rbind(mz=mz(x), intensity=intensity(x)))
# [[1]]
#           [,1] [,2] [,3] [,4]
# mz         1.5  2.5  3.5  4.5
# intensity  1.0  2.0  3.0  4.0
# 
# [[2]]
#           [,1] [,2] [,3] [,4] [,5]
# mz         1.5  2.5  3.5  4.5  5.5
# intensity  1.0  2.0  3.0  4.0  5.0

expected output:

# [[1]]
#           [,1] [,2] [,3] [,4] [,5]
# mz         1.5  2.5  3.5  4.5  5.5
# intensity  1.0  2.0  3.0  4.0  0.0
#
# [[2]]
#           [,1] [,2] [,3] [,4] [,5]
# mz         1.5  2.5  3.5  4.5  5.5
# intensity  1.0  2.0  3.0  4.0  5.0

[sgibb]

"Fixing" a bug (#137) by introducing two new bugs (#190, #191). Not too bad 😞 Hopefully I didn't introduced four new ones by fixing these two.

[lgatto]

Thanks for your work, @sgibb!