selectSamplesPeaks: Select fluorescence peaks for each sample.

Description Usage Arguments Details Value See Also Examples

View source: R/selectSamplesPeaks.R

Description

selectSamplesPeaks allows to select peaks for all samples.

Usage

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

Arguments

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

Details

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.

Value

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

See Also

samplesSelection

Examples

1
2
3
4
5
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)

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