simChIP {tileHMM} | R Documentation |
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).
data(simChIP)
A data frame with 210828 probe measurements under three different conditions with four replicates each.
chromosome
position
input_1
input_2
input_3
input_4
h3_1
h3_2
h3_3
h3_4
h3k27_1
h3k27_2
h3k27_3
h3k27_4
Humburg, P. and Bulger, D. and Stone, G. 2008 Parameter estimation for robust HMM analysis of ChIP-chip data. unpublished
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).
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)