Public CGH data of Snijders

Description

The data consist of 15 human cell strains with known karyotype (12 fibroblast cell strains, 2 chorionic villus cell strains, 1 lymploblast cell strain) from the NIGMS Human Genetics Cell Repository (http://locus.umdnj.edu/nigms). Each cell strain has been hybridized onto a CGH-array of 2276 BAC's spotted in triplicate.

Usage

data(snijders)

Source

http://www.nature.com/ng/journal/v29/n3/suppinfo/ng754_S1.html

References

A M Snijders, N Nowak, R Segraves, S Blackwood, N Brown, J Conroy, G Hamilton, A K Hindle, B Huey, K Kimura, S Law, K Myambo, J Palmer, B Ylstra, J P Yue, J W Gray, A N Jain, D Pinkel & D G Albertson , Assembly of microarrays for genome-wide measurement of DNA copy number, Nature Genetics 29, pp 263 - 264 (2001) Brief Communications.

Examples

data(snijders)
array <- gm13330

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(GLAD)

######################################################################################

Have fun with GLAD

For smoothing it is possible to use either
the AWS algorithm (Polzehl and Spokoiny, 2002,
or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics,  2008,

If you use the package with AWS, please cite:
Hupe et al. (Bioinformatics, 2004, and Polzehl and Spokoiny (2002,

If you use the package with HaarSeg, please cite:
Hupe et al. (Bioinformatics, 2004, and (Ben-Yaacov and Eldar, Bioinformatics, 2008,

For fast computation it is recommanded to use
the daglad function with smoothfunc=haarseg

######################################################################################

New options are available in daglad: see help for details.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GLAD/snijders.Rd_%03d_medium.png", width=480, height=480)
> ### Name: snijders
> ### Title: Public CGH data of Snijders
> ### Aliases: gm00143 gm01524 gm01535 gm01750 gm02948 gm03134 gm03563
> ###   gm03576 gm04435 gm05296 gm07081 gm07408 gm10315 gm13031 gm13330
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(snijders)
> array <- gm13330
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>