getInjectionPeak: Fit an injection peak to an FIA acquisition.
In proFIA: Preprocessing of FIA-HRMS data

Description Usage Arguments Value Examples

Determine an injection peak as an exponential modified gaussian function and a second order exponential corresponding to matrix effect to the most intense signals in an acquisition.

getInjectionPeak(
  xraw,
  bandlist,
  sec = 2,
  iquant = 0.95,
  gpeak = NULL,
  selIndex = NULL,
  scanmin = 1,
  scanmax = length(xraw@scantime),
  refinement = TRUE,
  graphical = FALSE
)

`xraw`	An xcmsRaw object as returned by `xcmsRaw`.
`bandlist`	A list of bands which can be used. Shall stay NULL in general use. bands will be determined automatically.
`sec`	A tolerance in sec to group the signals.
`iquant`	The maximum intensity intensity threshold under which the peaks would not be used for peak determination.
`gpeak`	An approximation of the injection peak, if NULL determining sizepeak.Geom will be used.
`selIndex`	A seleciton of index to make the regression. We recommend to let it to NULL.
`scanmin`	The first scan to consider for regression.
`scanmax`	The last scan to consider for regression.
`refinement`	Should the starting point of the regression be refined using the selected EICs.
`graphical`	shald the individually fitted components be plotted.

A vector contaning the injection peak

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)

  #Getting the injection scan
  gp <- determiningInjectionZone(xraw)

  #performing band detection.
  tbands <- findBandsFIA(xraw,ppm = 2,sizeMin = gp[3]-gp[1],beginning=gp[1],end=gp[2])

  #Getting the injection peak
  vpeak <- getInjectionPeak(xraw,bandlist=tbands,gpeak=gp)
  plot(vpeak,type="l")
}