make_spectrum_array: make_spectrum_array

In davidsbutcher/abundancer: Determine Abundances of 12C and 14N from Protein Mass Spectra

Description

Used to create a combined spectrum showing an experimental spectrum and peaks picked from a theoretical spectrum generated using a score matrix, sequence, optional PTM formula, charge, and resolving power.

Usage

make_spectrum_array(
  mz = NULL,
  intensity = NULL,
  SNR = 10,
  method = "MAD",
  refineMz = "kNeighbors",
  k = 2,
  score_array = NULL,
  sequence = NULL,
  PTMformula = "C0",
  charge = NULL,
  abund17O = c(0.00038),
  resolvingPower = 3e+05
)

Arguments

mz	A numeric vector containing m/z values for an experimental spectrum.
intensity	A numeric vector containing intensity values for an experimental spectrum.
SNR	Signal-to-noise cutoff to use for peak picking. See ?MSnbase::pickPeaks.
method	Method to use for peak picking. See '?MSnbase::pickPeaks'.
refineMz	Method for m/z refinement for peak picking. See ?MSnbase::pickPeaks.
k	Number of neighboring signals to use for m/z refinement if refineMz = "kNeighbors". See ?MSnbase::pickPeaks.
sequence	Sequence of the protein represented by the m/z and intensity vectors.
PTMformula	Chemical formula of PTMs of the proteoform represented by the m/z and intensity vectors. Formulas for all PTMs should be combined.
charge	Charge state of the proteoform represented by the m/z and intensity vectors.
resolvingPower	Resolving power to be used for generating the initial theoretical spectrum. This parameter does not need to match the resolving power of the experimental spectrum.
score_matrix	A matrix containing 12C and 14N abundances.

davidsbutcher/abundancer documentation built on Feb. 21, 2022, 2:13 p.m.