nuCpos-package: An R package for nucleosome positioning prediction

In nuCpos: An R package for prediction of nucleosome positions

Description

nuCpos, a derivative of NuPoP, is an R package for prediction of nucleosome positions. In nuCpos, a duration hidden Markov model is trained with a chemical map of nucleosomes either from budding yeast (Brogaard et al. (2012)), fission yeast (Moyle-Heyrman et al. (2012)), or mouse embryonic stem cells (Voong et al. (2016)). nuCpos outputs the Viterbi (most probable) path of nucleosome-linker states, predicted nucleosome occupancy scores and histone binding affinity (HBA) scores as NuPoP does. nuCpos can also calculate local and whole nucleosomal HBA scores for a given 147-bp sequence. Furthermore, effect of genetic alterations on nucleosome occupancy can be predicted with this package. The parental package NuPoP, which is based on an MNase-seq-based map of budding yeast nucleosomes, was developed by Ji-Ping Wang and Liqun Xi, licensed under GPL-2. Please refer to Xi et al. (2010) and Wang et al. (2008) for technical details of NuPoP.

Details

Package:	nuCpos
Type:	Package
Version:	1.5.1
Date:	2019-11-08
License:	GPL-2

predNuCpos: R function for prediction of nucleosome positioning, nucleosome occupancy and HBA scores.

HBA: R function for calculation of the histone binding affinity score of a whole nucleosome.

localHBA: R function for calculation of the local histone binding affinity.

mutNuCpos: R function for predicting the effect of a genetic alteration on nucleosome positioning.

Author(s)

Hiroaki Kato and Takeshi Urano

Maintainer: Hiroaki Kato<[e-mail]>

References

1. Wang JP, Fondufe-Mittendorf Y, Xi L, Tsai GF, Segal E and Widom J (2008). Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae. PLoS Computational Biology, 4(9):e1000175.

2. Xi L, Fondufe-Mittendorf Y, Xia L, Flatow J, Widom J and Wang JP (2010). Predicting nucleosome positioning using a duration hidden markov model. BMC Bioinformatics, 11:346

3. Brogaard K, Xi L, and Widom J (2012). A map of nucleosome positions in yeast at base-pair resolution. Nature, 486(7404):496-501.

4. Moyle-Heyrman G, Zaichuk T, Xi L, Zhang Q, Uhlenbeck OC, Holmgren R, Widom J and Wang JP (2013). Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning. Proc. Natl. Acad. Sci. U. S. A., 110(50):20158-63.

5. Ichikawa Y, Morohoshi K, Nishimura Y, Kurumizaka H and Shimizu M (2014). Telomeric repeats act as nucleosome-disfavouring sequences in vivo. Nucleic Acids Res., 42(3):1541-1552.

6. Voong LN, Xi L, Sebeson AC, Xiong B, Wang JP and Wang X (2016). Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping. Cell, 167(6):1555-1570.

7. Fuse T, Katsumata K, Morohoshi K, Mukai Y, Ichikawa Y, Kurumizaka H, Yanagida A, Urano T, Kato H, and Shimizu M (2017). Parallel mapping with site-directed hydroxyl radicals and micrococcal nuclease reveals structural features of positioned nucleosomes in vivo. Plos One, 12(10):e0186974.

Examples

    predNuCpos(file = system.file("extdata", "TRP1ARS1x1.fasta", 
        package = "nuCpos"), species = "sc", 
        ActLikePredNuPoP = TRUE)

## The prediction results are stored in the working directory.

Example output

/usr/lib/R/site-library/nuCpos/extdata/TRP1ARS1x1.fasta_Prediction4.txt was created in the working directory.

nuCpos documentation built on Nov. 8, 2020, 5:33 p.m.