timeLimits: Calculates time limits on the breath tracer

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

Calculates time limits on the breath tracer

Description

This function derives limits on the breath tracer indicated, where the intensity is greater than fracMaxTIC*max(tracer). By setting fracMaxTIC close to 1, the size of the limits will be restricted. This function also determine the index corresponding to the background, where variation between two successive point can be control with derivThreshold parameter.

Usage

timeLimits(
  object,
  fracMaxTIC = 0.5,
  fracMaxTICBg = 0.2,
  derivThresholdExp = 1,
  derivThresholdBg = 0.05,
  mzBreathTracer = NULL,
  minPoints = 2,
  degreeBaseline = 1,
  baseline = TRUE,
  redefineKnots = TRUE,
  plotDel = FALSE
)

## S4 method for signature 'ptrRaw'
timeLimits(
  object,
  fracMaxTIC = 0.6,
  fracMaxTICBg = 0.2,
  derivThresholdExp = 0.5,
  derivThresholdBg = 0.05,
  mzBreathTracer = NULL,
  minPoints = 2,
  degreeBaseline = 1,
  baseline = TRUE,
  redefineKnots = TRUE,
  plotDel = FALSE
)

## S4 method for signature 'ptrSet'
timeLimits(
  object,
  fracMaxTIC = 0.5,
  fracMaxTICBg = 0.2,
  derivThresholdExp = 1,
  derivThresholdBg = 0.05,
  minPoints = 2,
  degreeBaseline = 1,
  baseline = TRUE,
  redefineKnots = TRUE,
  plotDel = FALSE
)

Arguments

object	a ptrRaw or ptrSet object
fracMaxTIC	between 0 and 1. Percentage of the maximum of the tracer amplitude with baseline removal. If you want a finer limitation, increase fracMaxTIC, indeed decrease
fracMaxTICBg	same as fracMaxTIC but for background detection (lower than fracMaxTIC*max(TIC))
derivThresholdExp	the threshold of the difference between two successive points of the expiration
derivThresholdBg	the threshold of the difference between two successive points of the background
mzBreathTracer	NULL or a integer. Correspond to a nominal masses of Extract Ion Current (EIC) whose limits you want to compute. If NULL, the limits are calculated on the Total Ion Current (TIC).
minPoints	minimum duration of an expiration (in index).
degreeBaseline	the degree of polynomial baseline function
baseline	logical, should the trace be baseline corrected?
redefineKnots	logical, should the knot location must be redefined with the new times limits ?
plotDel	boolean. If TRUE, the trace is plotted with limits and threshold.

Value

a list with expiration limits (a matrix of index, where each column correspond to one expiration, the first row it is the beginning and the second the end, or NA if no limits are detected) and index of the background.

Examples

## ptrRaw object

library(ptairData)
filePath <- system.file('extdata/exhaledAir/ind1', 'ind1-1.h5',
package = 'ptairData')
raw <- readRaw(filePath)

timLim <- timeLimits(raw, fracMaxTIC=0.9, plotDel=TRUE)
timLim_acetone <- timeLimits(raw, fracMaxTIC=0.5, mzBreathTracer = 59,
plotDel=TRUE)

camilleroquencourt/ptairMS documentation built on June 9, 2024, 10:35 a.m.