calculate_score_matrix_dual: calculate_score_matrix_dual

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

Description

calculate_score_matrix_dual

Usage

calculate_score_matrix_dual(
  MSspectrum = NULL,
  mz = NULL,
  intensity = NULL,
  sequence = NULL,
  PTMformula = "C0",
  charge = 1,
  start12C = 0.987,
  start14N = 0.994,
  abundStepCoarse = 0.001,
  abundStepFine = 1e-04,
  SNR = 25,
  method = "MAD",
  refineMz = "kNeighbors",
  k = 2,
  resolvingPower = 3e+05,
  compFunc = "dotproduct",
  binSize = 0.05
)

Arguments

MSspectrum	An MSnbase Spectrum1 object.
mz	A numeric vector containing m/z values for a spectrum.
intensity	A numeric vector containing intensity values for a spectrum.
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.
start12C	Initial abundance of 12C to use for calculating the score matrix. Should be lower than the expected value.
start14N	Initial abundance of 14N to use for calculating the score matrix. Should be lower than the expected value.
abundStepCoarse	Abundance step to use for the coarse score matrix. Must be larger than abundStepFine.
abundStepFine	Abundance step to use for the fine score matrix. Must be smaller than abundStepCoarse.
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.
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.
compFunc	Function to use for comparison of experimental and theoretical spectra. Acceptable values are "dotproduct", "scoremfa", and "scoremfacpp".
binSize	Bin size to use for peak binning prior to comparing spectra. See ?MSnbase::bin.

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