determiningSizePeak.Geom: Determine the limits of the injection peak in a FIA...

Description Usage Arguments Value Examples

View source: R/findPeaksFIA.R

Description

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.

Usage

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

Arguments

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

Value

A triplet composed of c(left limit,right limit, maximum) of the estimated injection peak.

Examples

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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)
}

proFIA documentation built on March 20, 2021, 6 p.m.