MultiChIPmixHMM: an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates
1 INRA, UMR 518 MIA, F-75005 Paris, France
2 AgroParisTech, UMR 518 MIA, F-75005 Paris, France
3 INRA, UMR 1165 URGV, Evry, France
4 UEVE, UMR URGV, Evry, France
5 CNRS, ERL 8196 UMR URGV, Evry, France
6 Université de Rouen, LITIS EA 4108, Mont-Saint-Aignan, France
7 UMR de Génétique Végétale, INRA, Université Paris-Sud, CNRS, Gif-sur-Yvette, France
8 Innovative Methods of Computing, Center for Information Services and High Performance Computing, Technical University Dresden, Dresden, Germany
9 Cellular Networks and Systems Biology, Biotechnology Center, Technical University Dresden, Dresden, Germany
BMC Bioinformatics 2013, 14:271 doi:10.1186/1471-2105-14-271Published: 9 September 2013
Chromatin immunoprecipitation coupled with hybridization to a tiling array (ChIP-chip) is a cost-effective and routinely used method to identify protein-DNA interactions or chromatin/histone modifications. The robust identification of ChIP-enriched regions is frequently complicated by noisy measurements. This identification can be improved by accounting for dependencies between adjacent probes on chromosomes and by modeling of biological replicates.
MultiChIPmixHMM is a user-friendly R package to analyse ChIP-chip data modeling spatial dependencies between directly adjacent probes on a chromosome and enabling a simultaneous analysis of replicates. It is based on a linear regression mixture model, designed to perform a joint modeling of immunoprecipitated and input measurements.
We show the utility of MultiChIPmixHMM by analyzing histone modifications of Arabidopsis thaliana. MultiChIPmixHMM is implemented in R and including functions in C, freely available from the CRAN web site: http://cran.r-project.org webcite.