Man pages for ArnaudDroitLab/RJMCMC
Bayesian hierarchical model for genome-wide profiling of nucleosome positions based on high-throughput short-read data (MNase-Seq data)
| birthMove | Birth move when the current number of nucleosomes is superior... |
| birthMoveK1 | Birth move in the case that only one nucleosome is present |
| Bk | Birth Submove Probability |
| deathMove | Death move when more than one nucleosome are present |
| Dk | Death Submove Probability |
| elementWithHighestMode | Element with the hightest number of occurences |
| mergeAllRDSFiles | Merge nucleosome information |
| mergeAllRDSFilesFromDirectory | Merge nucleosome information from all RDS files present in a... |
| mergeRDSFiles | Merge nucleosome information for selected RDS files. |
| mhMove | Metropolis-Hastings move when more than one nucleosomes are... |
| mhMoveK1 | Metropolis-Hastings move when number of nucleosomes is equal... |
| normal.mixture | Normal Mixture Model |
| postMerge | A internal post treatment function to merge closely... |
| postTreatment | A post treatment function to merge closely positioned... |
| print.rjmcmcNucleosomes | Formated output of predicted nucleosomes |
| print.rjmcmcNucleosomesMerge | Formated output of predicted nucleosomes |
| priorMuDensity | Prior density of mu |
| reads_demo | Forward reads and reverse reads in 'numeric' format (for demo... |
| reads_demo_02 | Forward reads and reverse reads in 'integer' format (for demo... |
| RJMCMC | Nucleosome positioning mapping |
| rjmcmc-package | RJMCMC: Bayesian hierarchical model for genome-wide profiling... |
| RJMCMC_result | Nucleosomes obtained by running RJMCMC function (for demo... |
| student.mixture | Student Mixture Model |
| syntheticNucleosomeReads | Simulated dataset of reads generated by 'nucleoSim' package... |
| tnormale | Random deviate from a truncated normal distribution |
| validateDirectoryParameters | Parameters validation for the 'mergeAllRDSFilesFromDirectory'... |
| validateParameters | Parameters validation for the 'rjmcmc' function |
| validatePrepMergeParameters | Parameters validation for the 'postMerge' function |
| validateRDSFilesParameters | Parameters validation for the 'mergeRDSFiles' function |
