runCHR {RJMCMCNucleosomes} | R Documentation

## Run `rjmcmc` on multiples segments and merge results.

### Description

Run `rjmcmc` on a segment that is contained in a `list` of segments. Files generated by the function are all saved in a directory specified by user. A RData log file is created when a segment has been run while the result is saved in a RDS file.

If the same output directory is used more than once, the `rjmcmc` won't be called for segments that have the à corresponding RData log file.

### Usage

    runCHR(p, seg, niter, kmax, lambda, ecartmin, ecartmax, minReads,
      adaptNbrIterations, vSeed = -1, saveAsRDS = FALSE, dirOut = "out")

### Arguments

`p` | a `integer`, the position of the segment to treat in a `list` of `GRanges`.
`seg` | a `list` a `GRanges` containing the segments to be process.
`niter` | a positive `integer` or `numeric`, the number of iterations. Non-integer values of `nbrIterations` will be casted to `integer` and truncated towards zero.
`lambda` | a positive `numeric`, the theorical mean of the Poisson distribution. Default: 3.
`minReads` | a positive `integer` or `numeric`, the minimum number of reads in a potential canditate region. Non-integer values of `minReads` will be casted to `integer` and truncated towards zero. Default: 5.
`adaptNbrIterations` | a `logical` indicating if the number of iterations must be modified in function of the number of reads.
`vSeed` | a `integer`. A seed used when reproducible results are needed. When a value inferior or equal to zero is given, a random integer is used. Default: -1.
`saveAsRDS` | a `logical`. When `TRUE`, a RDS file containing the complete output of the c++ rjmcmc() function is created. Default : `FALSE`.
`kMax` | a positive `integer` or `numeric`, the maximum number of degrees of freedom per region. Non-integer values of `kMax` will be casted to `integer` and truncated towards zero.
`minInterval` | a `numeric`, the minimum distance between two nucleosomes.
`maxInterval` | a `numeric`, the maximum distance between two nucleosomes.
`maxLength` | a positive `integer` or `numeric`, the length of each segment.

### Value

0.

### Author(s)

Pascal Belleau, Astrid Deschenes

### Examples

    ## Load synthetic dataset of reads
    data(syntheticNucleosomeReads)

    ## Use dataset of reads to create GRanges object
    sampleGRanges <- GRanges(seqnames = syntheticNucleosomeReads$dataIP$chr,
        ranges = IRanges(start = syntheticNucleosomeReads$dataIP$start,
        end = syntheticNucleosomeReads$dataIP$end),
        strand = syntheticNucleosomeReads$dataIP$strand)

    # Segmentation of the reads
    seg <- segmentation(sampleGRanges, zeta = 147, delta = 50, maxLength = 1000)
    ## Not run:
    dir.create("out")
    dir.create("out/done")
    dir.create("out/results")

    runCHR(p=1, seg=seg, niter=1000, kmax=330,lambda=3,
                ecartmin=147, ecartmax=297, minReads=5)
    ## End(Not run)

[Package RJMCMCNucleosomes version 1.14.0 Index]