RJMCMC: Nucleosome positioning mapping

Description Usage Arguments Value Author(s) Examples

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.

Usage

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rjmcmc(startPosForwardReads, startPosReverseReads, nbrIterations, kMax,
  lambda = 3, minInterval, maxInterval, minReads = 5,
  adaptIterationsToReads = TRUE)

Arguments

startPosForwardReads

a vector of numeric, the start position of all the forward reads.

startPosReverseReads

a vector of numeric, the start position of all the reverse reads. Beware that the start position of a reverse read is always higher that the end positition.

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 nucleosomes 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.

Value

a list of class "rjmcmcNucleosomes" containing:

Author(s)

Rawane Samb, Pascal Belleau, Astrid Desch<c3><aa>nes

Examples

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## Loading dataset
data(reads_demo)

## Nucleosome positioning, running both merge and split functions
result <- rjmcmc(startPosForwardReads = reads_demo$readsForward,
         startPosReverseReads = reads_demo$readsReverse,
         nbrIterations = 1000, lambda = 2, kMax = 30,
         minInterval = 146, maxInterval = 292, minReads = 5)

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

## Print the position of nucleosomes
result$mu

ArnaudDroitLab/RJMCMC documentation built on Sept. 13, 2017, 5:48 a.m.