rjmcmc {RJMCMCNucleosomes} | R Documentation

## Nucleosome positioning mapping on a segment

### Description

Use of a fully Bayesian hierarchical model for chromosome-wide profiling of nucleosome positions based on high-throughput short-read data (MNase-Seq data). Beware that for a genome-wide profiling, each chromosome must be treated separatly. This function is optimized to run on segments that are smaller sections of the chromosome.

### Usage

    rjmcmc(reads, seqName = NULL, nbrIterations, kMax, lambda = 3, minInterval,
      maxInterval, minReads = 5, adaptIterationsToReads = TRUE, vSeed = -1,
      saveAsRDS = FALSE)

### Arguments

`reads` | a `GRanges` containing forward and reverse reads. Beware that the start position of a reverse read is always higher that the end positition.
`seqName` | a `character` string containing the label of the chromosome, present in the `GRanges` object, that will be used. The `NULL` value is accepted when only one seqname is present in the `GRanges`; the only seqname present will be used. Default: `NULL`.
`nbrIterations` | a positive `integer` or `numeric`, the number of iterations. Non-integer values of `nbrIterations` will be casted to `integer` and truncated towards zero.
`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.
`lambda` | a positive `numeric`, the theorical mean of the Poisson distribution. Default: 3.
`minInterval` | a `numeric`, the minimum distance between two nucleosomes.
`maxInterval` | a `numeric`, the maximum distance between two nucleosomes.
`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.
`adaptIterationsToReads` | a `logical` indicating if the number of iterations must be modified in function of the number of reads. Default: `TRUE`.
`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`.

### 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 `GRanges` containing the positions of the nucleosomes and '*' as strand. The `seqnames` of the `GRanges` correspond to the `seqName` input value. `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.

### Author(s)

Rawane Samb, Pascal Belleau, Astrid Deschenes

### Examples

    ## Loading dataset
    data(reads_demo_01)

    ## Nucleosome positioning, running both merge and split functions
    result <- rjmcmc(reads = reads_demo_01, seqName = "chr_SYNTHETIC",
                nbrIterations = 1000, lambda = 2, kMax = 30,
                minInterval = 146, maxInterval = 292, minReads = 5,
                vSeed = 10113, saveAsRDS = FALSE)

    ## Print the final estimation of the number of nucleosomes
    result$k

    ## Print the position of nucleosomes
    result$mu

    ## Print the maximum number of nucleosomes obtained during the iteration
    ## process
    result$k_max

[Package RJMCMCNucleosomes version 1.6.0 Index]