Normalize spectra and peaks

Usage

normalize(spec, peaks, normMeth, normMz, normTol)

Arguments

spec: List of MALDIquant::MassSpectrum or MALDIquant::MassPeaks objects
peaks: List of MALDIquant::MassPeaks
normMeth: Character, normalization method. Options are "TIC", "median" and "mz".
normMz: Numeric, mz used to normalize.
normTol: Numeric, tolerance around normMz.

Value

List of lists of normalized MALDIquant::MassSpectrum, normalized MALDIquant::MassPeaks, normalization factors as well as indicies of spectra containing the normMz in case of normMeth = "mz",

Details

Typically MassSpectrum lists should be provided as spec, still its possible to provide peaks for both arguments spec and peaks in the case that no raw data (continuous spectra) is available. In this case the operations performed on spec and peaks are equal.

Examples

data(Blank2022spec)
data(Blank2022peaks)
norm <- normalize(Blank2022spec, Blank2022peaks, normMeth = "mz", normMz = 760.585, normTol = 0.1)

# normalization factors
norm$factor 
#>     0     0     0     0  0.04  0.04  0.04  0.04  0.12  0.12  0.12  0.12  0.37 
#> 16141 17827 16463 15979 11687 14565 15224 11857  7949 13138 19570 13271 10036 
#>  0.37  0.37  0.37  1.11  1.11  1.11  1.11    10    10    10    10  3.33  3.33 
#> 12771 16056 16157 17366 14420 15080 18108 10366 17430 12866 14851 12895 14920 
#>  3.33  3.33    30    30    30    30 
#> 16715 13496  8735 14091 13168  7955