detectStartsInFile: Detects several starts in one file
In ChemoSens/PTRMSR: Analysis of PTRMS data

detectStartsInFile

R Documentation

Detects several starts in one file

Description

Detects several starts in one file (according to a vector of theoretical stimulation times)

Usage

detectStartsInFile(
  ptrFile_i,
  ion,
  startPeaks,
  endPeaks = NULL,
  methods = c("higherThanNoise", "startPeakProportion", "higherDerivative"),
  nPoints = 31,
  multiplyNoiseBy = 1.5,
  statOfNoise = "bl",
  smooth = TRUE,
  proportionOfMax = 0.1,
  peakChoice = "maxIntensity",
  order = 2,
  detectionThreshold = 15,
  firstAmongHighThreshold = 50,
  manual = NULL
)

Arguments

`ptrFile_i`	data frame exported from ptrViewer
`ion`	name of the column corresponding to the ion to analyse
`startPeaks`	a vector containing the stimulation times (theoretical starts) for all files
`endPeaks`	if NULL, the end of the peak period is given by the next start in startPeaks
`methods`	Choose among c("higherThanNoise","startPeakProportion","higherDerivative")
`nPoints`	number of points required in the smoothing function
`multiplyNoiseBy`	required if method='higherThanNoise' is chosen
`statOfNoise`	required if method='higherThanNoise'. Statistic to be multiplied by multiplyByNoise ('max' or 'avg'). Can also be 'bl' if corresponding to the estimation of noise during the whole evaluation or 'blper' if
`smooth`	If TRUE, the data is previously smoothed with the parameter halfWindowsSize
`proportionOfMax`	Number between 0 and 1. If method startPeakProportion is chosen and length(starts)==1, the starting time will be the first time that the intensity reaches this proportion of the maximale intensity of the peak. If length(starts) > 1, the starting time will be the minimum value obtained with this method for all starts.
`peakChoice`	"maxIntensity", "first" or "firstAmongHigh"
`order`	order of the derivative
`detectionThreshold`	intensity value to be reached to be considered as a peak (default to NULL corresponds to 0)
`firstAmongHighThreshold`	percentage of the maximum value to be reached in order to be considered as a peak when peak choice is firstAmongHigh
`manual`	manual results obtained (as a vector of the same length as startPeaks)