| 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). |