DnaAlteration: Cytosine methylation beta values for a sample of 198...
In FastHCS: Robust Algorithm for Principal Component Analysis

Description Usage Format Source Examples

A data frame with the subset of the 'Dna Alteration' data set corresponding to the sample of 'blood' and 'non-blood, non placenta' tissues.

1	data(DnaAlteration)

Labels: Observations with label "0" correspond to the subset of 'blood' tissues.
Column 2–1414: Cytosine methylation beta values collected at 1413 autosomal CpG loci.

Christensen, B.C Houseman, E.A. Marsit, C.J. Zheng, S. Wrench, M.R. Wiemels, J.L. Nelson, H.H. Karagas, M.R. Padbury, J.F. Bueno, R. Sugarbaker, D.J Yeh, R., Wiencke, J.K. Kelsey, K.T. (2009). Aging and Evnironemental Exposure Alter Tissue-Specific DNA Methylation Dependent upon CpG Island Context. PLoS Genet 5(8), e1000602.

data(DnaAlteration)
alpha<-0.5
Q<-15
p<-ncol(DnaAlteration[,-1])
ns<-FHCSnumStarts(q=Q,eps=(1-alpha)*4/5)
RunExample<-FALSE
if(RunExample){
	Fit<-FastHCS(x=DnaAlteration[,-1],q=Q,nSamp=ns,seed=0)
	colvec<-rep("orange",nrow(DnaAlteration))
	colvec[DnaAlteration[,1]==1]<-"blue"
	plot(Fit,col=colvec,pch=16)
}