| 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.
chromosomepositioninput_1input_2input_3input_4h3_1h3_2h3_3h3_4h3k27_1h3k27_2h3k27_3h3k27_4Humburg, 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 unpublished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)