R: Nucleosome positioning mapping on a segment

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 1.4.0 Index]