RJMCMC_result {RJMCMCNucleosomes} | R Documentation

## Nucleosomes obtained by running RJMCMC function using reads from reads_demo_02 dataset (for demo purpose).

### Description

A `list` of `class` "rjmcmcNucleosomes" which contains the information about the detected nucleosomes.

### Usage

    data(RJMCMC_result)

### Format

A `list` of `class` "rjmcmcNucleosomes" containing:

- `call` the matched call.

- `k` a `integer`, the final estimation of the number of nucleosomes. `0` when no nucleosome is detected.

- `mu` a `vector` of `numeric` of length `k`, the positions of the nucleosomes. `NA` when no nucleosome is detected.

- `k_max` a `integer`, the maximum number of nucleosomes obtained during the iteration process. `NA` when no nucleosome is detected.

### Value

A `list` of `class` "rjmcmcNucleosomes" containing:

- `call` the matched call.

- `k` a `integer`, the final estimation of the number of nucleosomes. `0` when no nucleosome is detected.

- `mu` a `vector` of `numeric` of length `k`, the positions of the nucleosomes. `NA` when no nucleosome is detected.

- `k_max` a `integer`, the maximum number of nucleosomes obtained during the iteration process. `NA` when no nucleosome is detected.

### See Also

- `rjmcmc` for profiling of nucleosome positions

- `rjmcmcCHR` for profiling of nucleosome positions for a large region. The function will take care of spliting and merging.

- `segmentation` for spliting a `GRanges` containing reads in a list of smaller segments for the `rjmcmc` function.

- `postTreatment` for merging closely positioned nucleosomes

- `mergeRDSFiles` for merging nucleosome information from selected RDS files.

- `plotNucleosomes` for generating a graph containing the nucleosome positions and the read coverage.

### Examples

    ## Loading dataset
    data(RJMCMC_result)
    data(reads_demo_02)

    ## Results before post-treatment
    RJMCMC_result$mu

    ## Post-treatment function which merged closely positioned nucleosomes
    postResult <- postTreatment(reads = reads_demo_02,
        extendingSize = 60, chrLength = 100000, resultRJMCMC = RJMCMC_result)

    ## Results after post-treatment
    postResult

[Package RJMCMCNucleosomes version 1.18.0 Index]