PreprocessMassSpectra {mssearchr} | R Documentation |
Pre-process mass spectra
Description
Pre-process mass spectra. Pre-processing includes rounding/binning, sorting, and normalization.
Usage
PreprocessMassSpectra(msp_objs, bin_boundary = 0.649, remove_zeros = TRUE)
Arguments
msp_objs |
A list of nested lists. Each nested list is a mass spectrum. Each nested
list must contain at least three elements: (1) the |
bin_boundary |
A numeric value. The position of a bin boundary (it can be considered as a
'rounding point'). The |
remove_zeros |
An integer value. If |
Details
Pre-processing includes the following steps:
Calculating a nominal mass spectrum. All floating point m/z values are rounded to the nearest integer using the value of the
bin_boundary
argument. Intensities of peaks with identical m/z values are summed.Intensities of mass spectral peaks are normalized to 999 (as it is done in the MS Search software).
Intensities of mass spectral peaks are rounded to the nearest integer.
If the
remove_zeros
argument isTRUE
, all zero-intensity peaks are removed from the mass spectrum.The
preprocessed
attribute is added and set toTRUE
for the respective mass spectrum.
Value
A list of nested lists. Each nested list is a mass spectrum. Only the
mz
and intst
elements of each nested list are
modified during the pre-processing step.
Examples
# Original mass spectra of chlorine and methane
msp_objs <- list(
list(name = "Chlorine",
mz = c(34.96885, 36.96590, 69.93771, 71.93476, 73.93181),
intst = c(0.83 * c(100, 32), c(100, 63.99, 10.24))),
list(name = "Methane",
mz = c(10, 11, 12, 13, 14, 15, 16, 17, 18, 19),
intst = c(0, 0, 25, 75, 155, 830, 999, 10, 0, 0))
)
matrix(c(msp_objs[[1]]$mz, msp_objs[[1]]$intst), ncol = 2) # Chlorine
matrix(c(msp_objs[[2]]$mz, msp_objs[[2]]$intst), ncol = 2) # Methane
# Pre-processed mass spectra of chlorine and methane
pp_msp_objs <- PreprocessMassSpectra(msp_objs, remove_zeros = TRUE)
matrix(c(pp_msp_objs[[1]]$mz, pp_msp_objs[[1]]$intst), ncol = 2) # Chlorine
matrix(c(pp_msp_objs[[2]]$mz, pp_msp_objs[[2]]$intst), ncol = 2) # Methane