ptrvIntensityByTime: ptrvIntensityByTime

In ChemoSens/PTRMSR: Analysis of PTRMS data

ptrvIntensityByTime

Description

Calculates the intensity by time for PTRViewer files. The calculation can be done by breathing cycle or on raw data.Breathing cycles are calculated on a reference ion (referenceBreath) with peak picking algorithms

Usage

ptrvIntensityByTime(
  dataset,
  timeCol = "RelTime",
  colToRemove = c("AbsTime", "Cycle"),
  correction = "none",
  referenceBreath = NULL,
  timePeriod = NULL,
  ions = NULL,
  funAggregate = "mean",
  total = FALSE,
  breathRatio = FALSE,
  minExpi = NULL,
  maxInspi = NULL,
  smoothMethodBreath = "MovingAverage",
  minimalDuration = 2,
  forMinExpiDivideMaxIntBy = 4,
  forMaxInspiDivideMaxIntBy = 5,
  halfWindowSize = 5,
  method = "MAD",
  SNR = 0,
  timeStart = 0
)

Arguments

dataset	whose names are timeCol, Ion1,... ,Ionp.
timeCol	name of the column of dataset containing the time
colToRemove	vector containing the names of the columns of datasets to be removed in the analysis (column that are neither the time nor ions names)
correction	"none" or "cycle". See Details.
referenceBreath	name of the ion taken as reference for breathing
timePeriod	vector containing starting and stopping point to get the statistics
ions	vector contatining all ions to be used in the analysis (by default all ions are used)
funAggregate	"mean", "maximal" or "sum"
total	if TRUE, the total intensity is calculated and added as a supplementary column
breathRatio	if TRUE, the ratio between the intensity of ion and the breath is calculated
minExpi	minimal value for an expiry intensity to be detected as an expiry (blue dotted line in the plot).
maxInspi	maximal intensity of the original curve required to be considered as a breathing peak (purple dotted line in the plot)
minimalDuration	minimalDuration of a breathing cycle (2 by default - as a accelerated breathing frequency corresponds to 20 cycles and more by minut and a low frequency is 12 and less -)
forMinExpiDivideMaxIntBy	default to 5. When minExpi is null, it is evaluated as the ratio of the maximal intensity and forMinIntensityDivideMaxIntBy
forMaxInspiDivideMaxIntBy	default to 5. When minExpi is null, it is evaluated as the ratio of the maximal intensity and forMinIntensityDivideMaxIntBy
halfWindowSize	parameter used to determine the smooth for the peak-picking used in break detection
method	method used for peak picking ("MAD" by default)
SNR	Signal noise ratio parameter used in peak picking
timeStart	timeStart is a value to be removed of the relTime column
removeNoise	if TRUE, the averaged intensity obtained during the timeBlank period is removed from the signal
smoothMethod	NULL, "SavitzkyGolay" or "MovingAverage"

Details

if 'cycle' is selected in correction option, the breathing cycles are calculated

Value

a list containing the obtained result (res), ggplot object containing different plots (gg) and, if correction='cycle' the cycle results are also added (detectCycle)

ChemoSens/PTRMSR documentation built on June 15, 2025, 10:40 a.m.