simChIP {tileHMM}R Documentation

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)

Format

A data frame with 210828 probe measurements under three different conditions with four replicates each.

chromosome
The chromosome targeted by probe. Here always ‘chr1’.
position
Position of central base.
input_1
Genomic DNA sample 1.
input_2
Genomic DNA sample 2.
input_3
Genomic DNA sample 3.
input_4
Genomic DNA sample 4.
h3_1
Histone H3 ChIP sample 1.
h3_2
Histone H3 ChIP sample 2.
h3_3
Histone H3 ChIP sample 3.
h3_4
Histone H3 ChIP sample 4.
h3k27_1
Histone H3K27me3 ChIP sample 1.
h3k27_2
Histone H3K27me3 ChIP sample 2.
h3k27_3
Histone H3K27me3 ChIP sample 3.
h3k27_4
Histone H3K27me3 ChIP sample 4.

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 unpublished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)
## Not run: 
## 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")
## End(Not run)

[Package tileHMM version 1.0-2 Index]