simChIP: Simulated ChIP-on-Chip Data

In tileHMM: Hidden Markov Models for ChIP-on-Chip Analysis

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 unpublished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)

tileHMM documentation built on May 30, 2017, 3:41 a.m.