determiningInjectionZone: First guess of the limit of the injection peak.

Description Usage Arguments Value Examples

View source: R/findPeaksFIA.R

Description

Determine a first approximation of the injection peak based on the angle of the injection peak and changing of variation. This peak is not used directly by findFIAsignal, but will be used to initialize the regression giving the injection peak. Shloud be used carefuly.

Usage

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determiningInjectionZone(xraw, threshold = 0.05, graphical = FALSE,
  scanmin = NULL, scanmax = NULL)

Arguments

xraw

An xcmsRaw object as returned by xcmsRaw. It may also be a TIC sequence as a list scan intensity.

threshold

A relative increase born to detect the limit of the injection peak.

graphical

should the resulting limit be plotted.

scanmin

The first scan to consider.

scanmax

The last scan to consider.

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 <- determiningInjectionZone(xraw)
}

adelabriere/proFIA documentation built on July 12, 2019, 5:46 a.m.