findClusters: Suggest clusters based on histograms

In beadarrayMSV: Analysis of Illumina BeadArray SNP data including MSV markers

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

Note

This is a “quick and dirty” way of estimating cluster centres. The function getCenters is used as a wrapper to findClusters and returns interpreted output after calling the latter function several times with different arguments

Author(s)

Lars Gidskehaug

See Also

getCenters, getSpecificCenters, createAlleleSet

Examples

## Not run: 
#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))

## End(Not run)

beadarrayMSV documentation built on May 1, 2019, 6:33 p.m.