getPeakList {ptairMS} | R Documentation

## get the peak list of a ptrSet object

### Description

get the peak list of a ptrSet object

### Usage

    getPeakList(set)

### Arguments

`set` | ptrSet object

### Value

a list of expressionSet, where:

- assay Data contains the matrix with m/z peak center in row names, and the quantification in cps at each time point

- feature Data the matrix with m/z peak center in row names, and the following columns:

  - quanti_unit: the mean of the quantification over the expiration/headspace time limits defined

  - background_unit: the mean of the quantification over the background time limits defined

  - diffAbs_unit: the mean of the quantification over the expiration/headspace time limits defined after subtracting the baseline estimated from the background points defined

  - pValLess/ pValGreater: the p-value of the unilateral t-test, who test that quantification (in cps) of expiration points are less/greater than the intensity of the background.

  - lower/upper: integration boundaries

  - parameter peak: estimated peak parameter

### Examples

    library(ptairData)
    dirRaw <- system.file("extdata/exhaledAir", package = "ptairData")
    exhaledPtrset <- createPtrSet(dir=dirRaw, setName="exhaledPtrset",
    mzCalibRef = c(21.022, 60.0525), fracMaxTIC = 0.7, saveDir = NULL )
    exhaledPtrset<-detectPeak(exhaledPtrset,mz=c(21,59))
    peakList<- getPeakList(exhaledPtrset )
    X<-Biobase::exprs(peakList[[1]])
    Y<- Biobase::fData(peakList[[1]])
    head(Y)

[Package ptairMS version 1.0.1 Index]