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


[Up] [Top]

Documentation for package ‘RJMCMCNucleosomes’ version 1.10.0

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).