Bladder cancer CGH data

Description

Bladder cancer data from 3 arrays CGH (Comparative Genomic Hybridyzation). Arrays dimension are 4 blocs per column, 4 blocs per row, 21 columns per bloc and 22 rows by blocs.

Usage

data(arrayCGH)

Format

A data frame composed of the following elements :

Log2Rat

Log 2 ratio.

Position

BAC position on the genome.

CHROMOSOME

Chromosome.

Col

Column location on the array.

Row

Row location on the array.

Source

Institut Curie, glad@curie.fr.

Examples

data(arrayCGH)
data <- array1 #array1 to array3

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/bladder.Rd_%03d_medium.png", width=480, height=480)
> ### Name: array
> ### Title: Bladder cancer CGH data
> ### Aliases: array1 array2 array3
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(arrayCGH)
> data <- array1 #array1 to array3
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>