getPeakList: get the peak list of a ptrSet object

In camilleroquencourt/ptairMS: Pre-processing PTR-TOF-MS Data

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)

camilleroquencourt/ptairMS documentation built on April 24, 2024, 9:03 p.m.