reads_demo_02 {RJMCMCNucleosomes} | R Documentation

## Forward reads and reverse reads in `GRanges` format (for demo purpose).

### Description

A group of forward and reverse reads that can be used to test the `rjmcmc` function.

### Usage

    data(reads_demo_02)

### Format

A `GRanges` containing forward and reverse reads.

### Value

A `GRanges` containing forward and reverse reads.

### 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(reads_demo_02)

    ## Nucleosome positioning
    ## Since there is only one chromosome present in reads_demo_02, the name
    ## of the chromosome does not need to be specified
    rjmcmc(reads = reads_demo_02, nbrIterations = 150, lambda = 3, kMax = 30,
                minInterval = 144, maxInterval = 290, minReads = 6)

[Package RJMCMCNucleosomes version 1.12.0 Index]