Simulated Gene Expression

Description

Gene expression profiles have been generated for 30 patients and 500 genes. Background correlation is set to 0.08 and the correlation for H1 regions to 0.5. The location of the H1 regions is as suggested in the work of Lai et al.(2005), i.e region 1 [101, 105], region 2 [201, 210], region 3 [301, 320] and region 4 [401, 440].

Usage

data("EXP_raw")

Format

Data frame containing the gene expression signal for 500 genes (rows) on 30 patients (columns).

References

Lai, W. R., Johnson, M. D., Kucherlapati, R., & Park, P. J. (2005). Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics, 21(19), 3763-3770.

Examples

data(EXP_raw)
G = cor(t(EXP_raw))## calculating the gene x gene correlation matrix
image(G)## plotting the correlation matrix

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(SegCorr)
Loading required package: cghseg
Loading required package: parallel
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/SegCorr/EXP_raw.Rd_%03d_medium.png", width=480, height=480)
> ### Name: EXP_raw
> ### Title: Simulated Gene Expression
> ### Aliases: EXP_raw
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(EXP_raw)
> G = cor(t(EXP_raw))## calculating the gene x gene correlation matrix
> image(G)## plotting the correlation matrix
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>