| Title: | An R package for prediction of nucleosome positions |
|---|---|
| Description: | nuCpos, a derivative of NuPoP, is an R package for prediction of nucleosome positions. nuCpos calculates local and whole nucleosomal histone binding affinity (HBA) scores for a given 147-bp sequence. Note: This package was designed to demonstrate the use of chemical maps in prediction. As the parental package NuPoP now provides chemical-map-based prediction, the function for dHMM-based prediction was removed from this package. nuCpos continues to provide functions for HBA calculation. |
| Authors: | Hiroaki Kato, Takeshi Urano |
| Maintainer: | Hiroaki Kato <[email protected]> |
| License: | GPL-2 |
| Version: | 1.25.0 |
| Built: | 2024-10-30 09:04:06 UTC |
| Source: | https://github.com/bioc/nuCpos |
nuCpos, a derivative of NuPoP, is an R package for prediction of nucleosome positions. nuCpos calculates local and whole nucleosomal histone binding affinity (HBA) scores for a given 147-bp sequence. Note: This package was designed to demonstrate the use of chemical maps in prediction. As the parental package NuPoP now provides chemical-map-based prediction, the function for dHMM-based prediction was removed from this package. Please refer to Xi et al. (2010) and Wang et al. (2008) for technical details of NuPoP. nuCpos continues to provide functions for HBA calculation. The models are based on chemical maps of nucleosomes from budding yeast (Brogaard et al. (2012)), fission yeast (Moyle-Heyrman et al. (2012)), or mouse embryonic stem cells (Voong et al. (2016)).
| Package: | nuCpos |
| Type: | Package |
| Version: | 1.17.4 |
| Date: | 2023-02-16 |
| License: | GPL-2 |
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.
Hiroaki Kato and Takeshi Urano
Maintainer: Hiroaki Kato<[email protected]>
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.
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
Brogaard K, Xi L, and Widom J (2012). A map of nucleosome positions in yeast at base-pair resolution. Nature, 486(7404):496-501.
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.
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.
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.
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.
load(system.file("extdata","inseq.RData",package="nuCpos")) HBA(inseq, species = "sc") localHBA(inseq, species = "sc")load(system.file("extdata","inseq.RData",package="nuCpos")) HBA(inseq, species = "sc") localHBA(inseq, species = "sc")
This function calculates the histone binding score for a given 147-bp sequence. Nucleosomal and linker models built upon the chemical maps are used for the calculation.
HBA(inseq, species = "mm", silent = FALSE)HBA(inseq, species = "mm", silent = FALSE)
inseq |
a character or DNAString object. The length of the character string must be 147 bp. |
species |
a character = mm, sc or sp; "mm" for mouse, "sc" for S. cerevisiae and "sp" for S. pombe. |
silent |
a logical value indicating whether messages are printed in the console. |
HBA outputs one numeric value:
histone binding affinity for a whole nucleosome.
load(system.file("extdata","inseq.RData",package="nuCpos")) HBA(inseq, species = "sc")load(system.file("extdata","inseq.RData",package="nuCpos")) HBA(inseq, species = "sc")
This function calculates local histone binding scores for 13 nucleosomal subsegments. Nucleosomal and linker models built upon the chemical maps are used for the calculation.
localHBA(inseq, species = "mm", silent = FALSE)localHBA(inseq, species = "mm", silent = FALSE)
inseq |
a character or DNAString object. The length of the character string must be 147 bp. |
species |
a character = mm, sc or sp; "mm" for mouse, "sc" for S. cerevisiae and "sp" for S. pombe. |
silent |
a logical value indicating whether messages are printed in the console. |
localHBA outputs a numeric vector of length 13:
local histone binding affinity scores for
specific regions in a nucleosome.
load(system.file("extdata","inseq.RData",package="nuCpos")) localHBA(inseq, species = "sc")load(system.file("extdata","inseq.RData",package="nuCpos")) localHBA(inseq, species = "sc")