#' This function reconstructs a Ms2 spectrum for all fragments with a correlation value bigger than a set cut-off
#'
#' @param precursor putative precursor peak
#' @param ms2dfCor corrected MS2 EICs
#' @param corValues calculated pearson correlations
#' @param CorCutOff cut-off for pearson correlation, default = 0.9
#'
#' @return returns a data frame containing the reconstructed MS2 spectrum
reconSpectrum <- function(precursor, ms2dfCor, corValues, CorCutOff = 0.9) {
#create empty data frame for MS2 spectrum
spectraDf <- data.frame()
#iterate through corrlation values and check if bigger than cut off
for(i in corValues$mz[which(corValues$corValue > CorCutOff)]) {
#get fitting EICs
rTime <- ms2dfCor$rtimeCor[which(ms2dfCor$mz == i)]
intensity <- ms2dfCor$intensityCor[which(ms2dfCor$mz == i)]
#get intensity at apex of MS1 peak
int <- approx(rTime, intensity, precursor[4])$y
#add to data frame
spectraDf <- rbind.data.frame(spectraDf,
cbind.data.frame(mz = i,
intensity = int,
corValue = corValues$corValue[which(corValues$mz == i)]))
}
#return spectrum as data frame
return(spectraDf)
}
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