findFIASignal: Detect peaks in an FIA acquisition.

Description Usage Arguments Value Examples

View source: R/findPeaksFIA.R

Description

Detect the peak corresponding to compounds present in the sample in a Flow Injection Analysis (FIA) acquisition. The item provided must be an xcmsRaw object.

Usage

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findFIASignal(xraw, ppm, es = NULL, solvar = c("throw", "keep"),
  solint = c("poly", "substract", "add"), fullInteg = FALSE, dmz = 0.001,
  graphical = FALSE, SNT = NULL, f = c("regression", "TIC"),
  pvalthresh = NULL, scanmin = 1, scanmax = length(xraw@scantime),
  bandCoverage = 0.3, shiftFactor = 0.3, sizeMin = NULL,
  bandlist = NULL, ...)

Arguments

xraw

An xcmsRaw object as returned by xcmsRaw.

ppm

The authorized deviation between scans in ppm, this parameter will also be used to fuse the bands if there are close enough.

es

A noise estimation object as returned by estimateNoiseMS, or NULL if the parameter noise if only an threshold is supposed to be used.

solvar

Should the signal corresponding to solvent be kept ? Only their maximum intensiyt will be calculated.

solint

How are the intensity of signal with bot solvent and sample be treated in the injection zone region, the area of the rectangle with peak-width and solvent intensity is considered.

fullInteg

If no solvent is detected before the injection, should the signals be integrated on the ufll chromatogram.

  • poly. Half of this area is kept.

  • substract. The area is removed substracted.

  • remove. The area is conserved in the final value.

dmz

The minimum absolute value of the deviation between scans, to take into account the higher diviations at low masses.

graphical

A boolean indicating if the detected area shall be plotted.

SNT

NULL by default a relative intensity of signal/intensity of solvent threshold, used only if es is equal to NULL.

f

method to design the filter, "TIC" means that the peak of the TIC is used as a filter. "regression" means that the signal is regressed form the most intense band as an Exponential modified gaussian.

pvalthresh

The threshold used in p-value to discard signal, only used if a noise model is provided.

scanmin

The first scan to consider.

scanmax

The last scan to consider.

bandCoverage

A filter on the number of point found in a band. 0.3 by default to allow matrix effect.

sizeMin

The minimum number of point considered for a band to be considred for solvent filtration.

bandlist

An optional bandlist to be passed.

...

more arguments to be passed to the determiningInjectionZone function.

Value

A numeric matrix with the following column

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)

  ppm<-2

  #getting the filtered signals without noise model which is not recommended.
  tsignal<-findFIASignal(xraw,ppm=ppm,SNT=3)

  #Getting the noise model un the plasSet object.
  data(plasSet)
  es<-attr(plasSet,"noiseEstimation")

  #Getting the signal with a noise model.
  tsignal<-findFIASignal(xraw,ppm=2,es=es,pvalthresh=0.005)
  head(tsignal)
}

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