peaksSelection: Select fluorescence peaks.

Description Usage Arguments Details Value See Also Examples

View source: R/peaksSelection.R

Description

peaksSelection allows to identify peaks for the defined channel.

Usage

1
2
3
peaksSelection(data, channel = "green", metric = "median", Nchannel = NA,
  baseThr = 0.01, minLength = 10, discartPeaks = NA,
  discartPeaksPerc = 1)

Arguments

data

data to be analyzed (formatted as data.frame with 4 columns: green, orange, blue, time)

channel

channel to be considered, default="green"

metric

metric to be used to define the value to assign to each peak, select among "median", "mean", "max" or "AUC", default is "median"

Nchannel

channel to be used to normalise data, default is NA (raccomended to not use it)

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

Details

This function reads the data produced with labview in the 3 channels (green, orange and blue) and selects the peaks corresponding to the plugs in the user defined channel. This is done by considering as peaks the signal that goes above a threshold (defined by argument "baseThr") and stays above for a minimum number of data points (defined by argument "minLength").

Value

This function returns a 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

See Also

plotData

Examples

1
2
data(BxPC3_data,package="BraDiPluS")
peaks <- peaksSelection(data=MyData, channel="blue")

saezlab/BraDiPluS documentation built on May 20, 2018, 4:42 a.m.