Cytosine methylation beta values for a sample of 198 non-pathological human tissue specimens.

Description

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

Usage

DnaAlteration

Format

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.

Source

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.

Examples

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)
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(FastHCS)
Loading required package: matrixStats
matrixStats v0.50.2 (2016-04-24) successfully loaded. See ?matrixStats for help.
Loading required package: robustbase

Attaching package: 'robustbase'

The following objects are masked from 'package:matrixStats':

    colMedians, rowMedians

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/FastHCS/DnaAlteration.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DnaAlteration
> ### Title: Cytosine methylation beta values for a sample of 198
> ###   non-pathological human tissue specimens.
> ### Aliases: DnaAlteration
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 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)
+ }
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>