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

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Documentation for package ‘RJMCMCNucleosomes’ version 1.32.0

• 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).