determiningSizePeak.Geom: Determine the limits of the injection peak in a FIA...
In adelabriere/proFIA: Preprocessing of FIA-HRMS data

Description Usage Arguments Value Examples

Determine a first approximation of the injection peak using the Douglas-Peuker Algorithm provided in the rgeos package. The object provided must be an xcmsRaw object.

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determiningSizePeak.Geom(xraw, scanmin = 1, scanmax = length(xraw@scantime),
  freq = 0.15, graphical = FALSE, smooth = TRUE, extended = FALSE,
  percentSol = NULL)

`xraw`	An xcmsRaw object as returned by `xcmsRaw`.
`scanmin`	The minimum scan to consider for peak detection.
`scanmax`	the maximum scan to consider. injection peak detection.
`freq`	The degrees of smoothing used on the TIC, corresponding to the cutting frequency of the blackman windowed sync filter.
`graphical`	should the resulting peak be plotted.
`smooth`	Should the TIC be smoothed, recommended.
`extended`	In case of very long tailing, shloud the research be extended.
`percentSol`	If extended is TRUE, the limiting level of solvent for

A triplet composed of c(left limit,right limit, maximum) of the estimated 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 a first approximation of injection peak;
  sp <- determiningSizePeak.Geom(xraw)
}