Object of Class arrayCGH

Description

Description of the object arrayCGH.

Value

The object arrayCGH is a list with at least a data.frame named arrayValues and a vector named arrayDesign. The data.frame arrayValues must contain the following fields :

The vector arrayDesign is composed of 4 values : c(arrayCol, arrayRow, SpotCol, SpotRow). The array CGH is represented by arrayRow*arrayCol blocs and each bloc is composed of SpotRow*SpotCol spots.

N.B. : Col takes the values in 1:arrayRow*SpotRow and Row takes the values in 1:arrayCol*SpotCol

Note

People interested in tools dealing with array CGH analysis can visit our web-page http://bioinfo.curie.fr.

Author(s)

Philippe Hupé, glad@curie.fr.

See Also

glad.

Examples

data(arrayCGH)

# object of class arrayCGH

array <- list(arrayValues=array2, arrayDesign=c(4,4,21,22))
class(array) <- "arrayCGH"

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/arrayCGH.Rd_%03d_medium.png", width=480, height=480)
> ### Name: arrayCGH
> ### Title: Object of Class arrayCGH
> ### Aliases: arrayCGH
> ### Keywords: classes
> 
> ### ** Examples
> 
> data(arrayCGH)
> 
> # object of class arrayCGH
> 
> array <- list(arrayValues=array2, arrayDesign=c(4,4,21,22))
> class(array) <- "arrayCGH"
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>