README.md

In saezlab/BraDiPluS: BraDiPluS - Braille Display Plugs Data Analysis

BraDiPluS

BraDiPluS - Braille Display Plugs Data Analysis - is an R package developed to analyse the data of plugs produced using in-house combinatorial microfluidics platform and adquired using an in-house LabVIEW program (written by R. Utharala) allowing the detection of three channels: blue: sample barcodes green: Caspase-3 activity assay * orange: marker dye to monitor mixing of reagents

For extended documentation of BraDiPluS please refer to https://saezlab.github.io/BraDiPluS/

How to install it

Open R and, from the folder with the package, type:

install.packages('BraDiPluS',repos=NULL,type='src')

Workflow example

Load the example data provided in the package

data("BxPC3_data", package="BraDiPluS")
data("sampleNames", package="BraDiPluS")

plot the data

plotData(data=MyData, channels=c("blue", "orange", "green"))

separate the different samples (separated by barcode)

res <- samplesSelection(data=MyData, BCchannel="blue",BCthr=0.01, BCminLength=100, distThr=16, plotMyData=F, barcodePos="before")
samples<-res$samples
names(samples)<-sampleNames

plotData(data=MyData, channels=c("blue", "orange", "green"), samples = samples)

select the peaks for each sample

samplesPeaks <- selectSamplesPeaks(samples, channel="green", metric="median", baseThr=0.01, minLength=350, discartPeaks="first", discartPeaksPerc=5)

remove outliers based on orange channel

runs<-list(run1=samplesPeaks)
runs.qa<-qualityAssessment(runs=runs)

look at the median sample values

allData<-do.call(cbind, lapply(runs.qa, function(myRun){
sapply(sapply(myRun, get, x="green"), median)
}))

compute z-score

allData_scale<-apply(allData,2,scale)

saezlab/BraDiPluS documentation built on May 29, 2019, 12:56 p.m.