findFIASignal: Detect peaks in an FIA acquisition.
In adelabriere/proFIA: Preprocessing of FIA-HRMS data

Description Usage Arguments Value Examples

Detect the peak corresponding to compounds present in the sample in a Flow Injection Analysis (FIA) acquisition. The item provided must be an xcmsRaw object.

findFIASignal(xraw, ppm, es = NULL, solvar = c("throw", "keep"),
  solint = c("poly", "substract", "add"), fullInteg = FALSE, dmz = 0.001,
  graphical = FALSE, SNT = NULL, f = c("regression", "TIC"),
  pvalthresh = NULL, scanmin = 1, scanmax = length(xraw@scantime),
  bandCoverage = 0.3, shiftFactor = 0.3, sizeMin = NULL,
  bandlist = NULL, ...)

`xraw`	An xcmsRaw object as returned by `xcmsRaw`.
`ppm`	The authorized deviation between scans in ppm, this parameter will also be used to fuse the bands if there are close enough.
`es`	A noise estimation object as returned by estimateNoiseMS, or NULL if the parameter noise if only an threshold is supposed to be used.
`solvar`	Should the signal corresponding to solvent be kept ? Only their maximum intensiyt will be calculated.
`solint`	How are the intensity of signal with bot solvent and sample be treated in the injection zone region, the area of the rectangle with peak-width and solvent intensity is considered.
`fullInteg`	If no solvent is detected before the injection, should the signals be integrated on the ufll chromatogram. poly. Half of this area is kept. substract. The area is removed substracted. remove. The area is conserved in the final value.
`dmz`	The minimum absolute value of the deviation between scans, to take into account the higher diviations at low masses.
`graphical`	A boolean indicating if the detected area shall be plotted.
`SNT`	NULL by default a relative intensity of signal/intensity of solvent threshold, used only if es is equal to NULL.
`f`	method to design the filter, "TIC" means that the peak of the TIC is used as a filter. "regression" means that the signal is regressed form the most intense band as an Exponential modified gaussian.
`pvalthresh`	The threshold used in p-value to discard signal, only used if a noise model is provided.
`scanmin`	The first scan to consider.
`scanmax`	The last scan to consider.
`bandCoverage`	A filter on the number of point found in a band. 0.3 by default to allow matrix effect.
`sizeMin`	The minimum number of point considered for a band to be considred for solvent filtration.
`bandlist`	An optional bandlist to be passed.
`...`	more arguments to be passed to the determiningInjectionZone function.

A numeric matrix with the following column

mzmin the minimum value of the mass traces in the m/z dimension.
mzmax the maximum value of the mass traces in the m/z dimension.
scanMin the first scan on which the signal is detected.
scanMax the last scan on which the signal is detected.
areaIntensity the integrated area of the signal.
maxIntensity the maximum intensity of the signal.
solventIntensity the intensity of the solvent, 0 means that no significant solvent was detected.
corPeak An idicator of matrix effect, if it's close to 1, the compound does not suffer from heavy matrix effect, if it is inferior to 0.5, the compound suffer from heavy matrix effect.
timeShifted An indicator of the shifting of th epeak in the time direction.
signalOverSolventRatio The ratio of the signal max intensity on the solvent max intensity.

if(require(plasFIA)){
  #Getting the path of a file.
  path_raw<-list.files(system.file(package="plasFIA","mzML"),full.names=TRUE)[2]

  #Opening the file with xcms
  xraw<-xcmsRaw(path_raw)

  ppm<-2

  #getting the filtered signals without noise model which is not recommended.
  tsignal<-findFIASignal(xraw,ppm=ppm,SNT=3)

  #Getting the noise model un the plasSet object.
  data(plasSet)
  es<-attr(plasSet,"noiseEstimation")

  #Getting the signal with a noise model.
  tsignal<-findFIASignal(xraw,ppm=2,es=es,pvalthresh=0.005)
  head(tsignal)
}