beadarrayMSV (version 1.0.3)

findClusters: Suggest clusters based on histograms

Description

Initial cluster centres are suggested based on the theta values of a single marker. Usually called by getCenters or getSpecificCenters

Usage

findClusters(theta, breaks = seq(-0.25, 1.25, 0.05), minBin = 2,
    plot = FALSE)

Arguments

theta

Numeric vector of polar coordinates angles for a single marker, as given in the assayData slot theta of objects of class "AlleleSetIllumina"

breaks

Histogram breakpoints. See hist

minBin

The minimum peak height below which peaks are set to zero

plot

If TRUE, histogram is plotted (for testing)

Value

• A list containing
• clPeaks
  Suggested cluster centres
• clSizes
  Estimated number of samples in each cluster
• nCl
  Number of clusters

See Also

getCenters, getSpecificCenters, createAlleleSet

Examples

#Read pre-processed data directly into AlleleSetIllumina object
rPath <- system.file("extdata", package="beadarrayMSV")
dataFiles <- makeFilenames('testdata',normOpts,rPath)
beadFile <- paste(rPath,'beadData_testdata.txt',sep='/')
beadInfo <- read.table(beadFile,sep='\t',header=TRUE,as.is=TRUE)
BSRed <- createAlleleSetFromFiles(dataFiles[1:4],markers=1:10,beadInfo=beadInfo)

#Tune resolution or filter to achieve monomorphic marker
print(findClusters(assayData(BSRed)$theta[1,],plot=TRUE))
print(findClusters(assayData(BSRed)$theta[1,],breaks=seq(-0.25,1.25,0.1),plot=TRUE))
print(findClusters(assayData(BSRed)$theta[1,],minBin=5,plot=TRUE))

#Tune resolution to achieve MSV-5 call
par(mfrow=c(3,1),mai=c(.5,.5,.5,.1))
plot(assayData(BSRed)$theta[2,],assayData(BSRed)$intensity[2,],pch='o')
print(findClusters(assayData(BSRed)$theta[2,],plot=TRUE))
print(findClusters(assayData(BSRed)$theta[2,],breaks=seq(-0.25,1.25,0.04),plot=TRUE))