selectSamplesPeaks: Select fluorescence peaks for each sample.
In saezlab/BraDiPluS: BraDiPluS - Braille Display Plugs Data Analysis

Description Usage Arguments Details Value See Also Examples

selectSamplesPeaks allows to select peaks for all samples.

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selectSamplesPeaks(samples, channel = "green", metric = "median",
  Nchannel = NA, baseThr = 0.01, minLength = 10, discartPeaks = NA,
  discartPeaksPerc = 1)

`samples`	samples as output of the function `samplesSelection`
`channel`	channel to be considered, default="green"
`metric`	metric to be used, selct among "median", "mean", "max" or "AUC", default is median
`Nchannel`	channel to be used to normalise data, default is NA (use not recommended)
`baseThr`	threshold on the baseline used in order to define what is a peak, default is 0.01
`minLength`	minimum length of a plug/droplet in number of data points, default is 10 (note that unit is number of data points, not seconds)
`discartPeaks`	select of to discart first and/or last peak ("first" discart the first, "last" discart the last, "both" discart both), default is NA
`discartPeaksPerc`	select the percentage of peaks to discart if discartPeaks is defined. Default is 1

This function select the peaks for all the samples previously identified using samplesSelection by applying the function peaksSelection to the data corresponding to the different samples.

This function returns a list with, in each positions peaks for the corrsponding samples. Peaks are organized as data.frame with one peak for each row and 9 columns:

green: value of the peak in the green channel
orange: value of the peak in the orange channel
blue: value of the peak in the blue channel
norm: value of the selected channel normalized by the value of the Nchannel, if the Nchannel is provided (otherwise the value is set to 0)
start: starting point of the peak
end: final point of the peak
length: length of the peak

samplesSelection

data(BxPC3_data,package="BraDiPluS")
res <- samplesSelection(data=MyData, BCchannel="blue", 
BCthr=0.01, distThr=300, plotMyData=TRUE)
samples <-res$samples
samplesPeaks <- selectSamplesPeaks(samples, channel="green", metric="median", baseThr=0.01, minLength=350, discartPeaks="first", discartPeaksPerc=5)