getInjectionPeak {proFIA} | R Documentation

## Fit an injection peak to an FIA acquisition.

### Description

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.

### Usage

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

### Arguments

`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.

### Value

A vector contaning the injection peak

### Examples

    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")
    }

[Package proFIA version 1.12.0 Index]