characterize_peak: characterize_peak

In MGMS2: 'MGMS2' for Polymicrobial Samples

Description

This function characterizes peaks by species/strain in a simulated spectrum after taking the highest peak or merging peaks in each bin.

Usage

characterize_peak(spec, option = 1, bin.size = 1, min.mz = 1000, max.mz = 2200)

Arguments

spec	A data frame that contains m/z values of peaks, normalized intensities of peaks, species names, and strain names. Either an output of simulate_poly_spectra or one elements of a list output from simulate_many_poly_spectra.
option	An option on how to merge peaks. There are two options: 1) no merge, thus take the highest intensity peak in each bin after binning a spectrum by bin.size, or 2) take a sum of intensity within each bin after binning a spectrum by bin.size.
bin.size	An integer. A bin size. (1 by default)
min.mz	A real number. Minimum mass-to-charge ratio. (1000 by default)
max.mz	A real number. Maximum mass-to-charge ratio. (2200 by default)

Value

A data frame that contains m/z values of peaks (mz), intensities of peaks (int), species names (species), and strain names (strain). Species and strain columns may contain more than one species/strain if an option 2 is chosen.

Examples

spectra.processed.A <- process_monospectra(
   file=system.file("extdata", "listA.txt", package="MGMS2"),
   mass.range=c(1000,2200))
spectra.processed.B <- process_monospectra(
   file=system.file("extdata", "listB.txt", package="MGMS2"),
   mass.range=c(1000,2200))
spectra.processed.C <- process_monospectra(
   file=system.file("extdata", "listC.txt", package="MGMS2"),
   mass.range=c(1000,2200))
spectra.mono.summary.A <- summarize_monospectra(
   processed.obj=spectra.processed.A,
   species='A', directory=tempdir())
spectra.mono.summary.B <- summarize_monospectra(
   processed.obj=spectra.processed.B,
   species='B', directory=tempdir())
spectra.mono.summary.C <- summarize_monospectra(
   processed.obj=spectra.processed.C,
   species='C', directory=tempdir())
mono.info=gather_summary(c(spectra.mono.summary.A, spectra.mono.summary.B, spectra.mono.summary.C))
mixture.ratio <- list()
mixture.ratio['A']=1
mixture.ratio['B']=0.5
mixture.ratio['C']=0
sim.template <- create_insilico_mixture_template(mono.info)
insilico.spectrum <- simulate_poly_spectra(sim.template, mixture.ratio)
merged.spectrum <- characterize_peak(insilico.spectrum, option=2) 

MGMS2 documentation built on April 24, 2020, 9:06 a.m.