# Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)

## Documentation for package ‘RJMCMCNucleosomes’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

RJMCMCNucleosomes-package | RJMCMCNucleosomes: Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
mergeAllRDSFilesFromDirectory | Merge nucleosome information from all RDS files present in a same directory. Beware that only nucleosome information from same chromosome should be merged together.
mergeRDSFiles | Merge nucleosome information from selected RDS files.
plotNucleosomes | Generate a graph of nucleosome positions with read coverage
postTreatment | A post-treatment function to merge closely positioned nucleosomes, from the same chromosome, identified by the 'rjmcmc' function.
print.rjmcmcNucleosomes | Formated output of predicted nucleosomes
print.rjmcmcNucleosomesBeforeAndAfterPostTreatment | Formated output of predicted nucleosomes
print.rjmcmcNucleosomesMerge | Formated output of predicted nucleosomes
reads_demo_01 | Forward reads and reverse reads in 'GRanges' format (for demo purpose).
reads_demo_02 | Forward reads and reverse reads in 'GRanges' format (for demo purpose).
rjmcmc | Nucleosome positioning mapping on a segment
rjmcmcCHR | Nucleosome positioning mapping on a large segment, up to a chromosome
RJMCMCNucleosomes | RJMCMCNucleosomes: Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
RJMCMC_result | Nucleosomes obtained by running RJMCMC function using reads from reads_demo_02 dataset (for demo purpose).
segmentation | Split a 'GRanges' containing reads in a list of smaller segments for the 'rjmcmc' function.
syntheticNucleosomeReads | Simulated dataset of reads generated by 'nucleoSim' package (for demo purpose).