compare profile to centroid methods

[cpanse]

#R

# Orbitrap Fusion Lumos FSN20242
rawfile <- "/Users/cp/Downloads/p2722/stds_pos_neg_MS_highconc_UVPD_50_300.raw"


library(MsBackendRawFileReader)

be <- backendInitialize(MsBackendRawFileReader(), files = rawfile)
(SP <- Spectra(be))

i.p <- Spectra::intensity(SP)
m.p <- Spectra::mz(SP)

SC <- Spectra::pickPeaks(SP)
i.c <- Spectra::intensity(SC)
m.c <- Spectra::mz(SC)


idx.ms2 <-  which(msLevel(SP) == 2)

# BiocManager::install('cpanse/protViz')
# protViz package version >= 0.3.6
library(protViz)

rv <- lapply(idx.ms2, function(i){
        profile <- data.frame(mZ=m.p[[i]], intensity=i.p[[i]])
        rv.protViz <- protViz::centroid(m.p[[i]], i.p[[i]])
        rv.spectra  <- data.frame(mZ=m.c[[i]], intensity=i.c[[i]])

        if (nrow(rv.protViz) == nrow(rv.spectra )){
                fit <- lm(rv.protViz$mZ ~ rv.spectra$mZ)
        list(profile, rv.protViz, rv.spectra, fit)
        }
        list(profile, rv.protViz, rv.spectra)

})