samplesSelection: Separate data in samples (i.e. experimental conditions).
In saezlab/BraDiPluS: BraDiPluS - Braille Display Plugs Data Analysis

Description Usage Arguments Details Value See Also Examples

samplesSelection define samples using the barcoding channel to separate them.

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samplesSelection(data, channel = "green", BCchannel = "blue",
  BCthr = 0.05, distThr = 16, plotMyData = FALSE, BCminLength = 100,
  barcodePos = "after")

`data`	data to be analyzed (formatted as data.frame with 4 columns: green, orange, blue, time)
`channel`	channel(s) to be visualized, which is in general the main channel with the data. Default="green"
`BCchannel`	channel used for barcoding, default is "blue"
`BCthr`	threshold used in order to define what is a peak in the barcoding channel. Default is 0.05
`distThr`	minimum duration of a sample (the unit is "time" as defined in the data)
`plotMyData`	TRUE to show the plot of the data, FALSE not to show it. If data are large plotting can take seconds/minutes
`BCminLength`	minimum length of a plug in number of data points for the barcoding channel, default is 100 (note that unit here is number of data points, not "time")
`barcodePos`	specify if the barcode is before or after the sample ("before" or "after"), default is "after"

This function allows to select the samples using the selected barcoding channel to separate replicates (peaks) from different experimental conditons. This function first detect the barcoding peaks (in the channel defined by "BCchannel") and that is done considering the blue signal that goes above a defined threshold (which is the “BCthr” argument) and with a minimum width (defined by "BCminLength" argument). Then it looks at the space between selected blue peaks and considers as samples those with a distance higher than a threshold (defined by "distThr").

This function returns a list with two components:

samples: list containing samples as elements. Each sample is a data.frame with the same structure of the input data
barcode: corresponding barcode for each sample. Each barcode is a data.frame with the same structure of the input data

selectSamplesPeaks to select the peaks in each sample

data(BxPC3_data,package="BraDiPluS")
res <- samplesSelection(data=MyData, BCchannel="blue",BCthr=0.01,
BCminLength=100, distThr=16, barcodePos="before")
samples <-res$samples
barcode <-res$barcode