tileHMM (version 1.0-2)

simChIP: Simulated ChIP-on-Chip Data

Description

A simulated ChIP-on-chip dataset. This is part of the data used in a simulation study by Humburg et al. (2007), it is based on data published by Zhang et al. (2007).

Usage

data(simChIP)

source

Humburg, P. and Bulger, D. and Stone, G. 2008 Parameter estimation for robust HMM analysis of ChIP-chip data. unpublished

References

Zhang, X. and Clarenz, O. and Cokus, S. and Bernatavichute, Y. V. and Goodrich, J. and Jacobsen S. E. 2007 Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biology, 5(5).

Examples

data(simChIP)
## scatter plots
library(geneplotter)
simChIP[ , 3:14] <- logb(simChIP[ , 3:14], 2)
par(mfrow=c(2,2))
smoothScatter(simChIP[ , 7], simChIP[ , 11], xlab = "H3 sample 1", 
    ylab = "H3K27me3 sample 1")
smoothScatter(simChIP[ , 8], simChIP[ , 12], xlab = "H3 sample 2", 
    ylab = "H3K27me3 sample 2")
smoothScatter(simChIP[ , 9], simChIP[ , 13], xlab = "H3 sample 3", 
    ylab = "H3K27me3 sample 3")
smoothScatter(simChIP[ , 10], simChIP[ , 14], xlab = "H3 sample 4", 
    ylab = "H3K27me3 sample 4")