rjmcmcNucleo: Interface for the RJMCMC nucleosome mapping method in C++

In RJMCMCNucleosomes: Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)

Description

Function that calls the core of the nucleosome positioning mapping function that is implemented in C++.

Usage

rjmcmcNucleo(startPosForwardReads, startPosReverseReads, nbrIterations, kMax,
  lambda, minInterval, maxInterval, minReads = 5L,
  adaptIterationsToReads = TRUE, vSeed = -1)

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.
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.

Value

a list containing:

• k a integer, the number of nucleosomes.

• k_max a integer, the maximum number of nucleosomes obtained during the iteration process.

• it a vector of integer of length k, the variance of the forward reads for each nucleosome.

• nbState a integer, the number of changes of state.

• mu a matrix of numeric with k_max columns and nbState row containing, in each row, the mu values associated the the state identified by the row number.

• muHat a matrix of numeric with k_max columns and k_max rows containing, in each row, the mean mu values associated the number of nucleosomes detected. The row number corresponds to the number of nucleosomes detected.

• nbK a vector of length k_max containing integer, the number of iterations which detected a specific number of nucleosomes. The position in the vector correspond to the number of nucleosomes.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

data(reads_demo_01)

forward <- start(reads_demo_01[strand(reads_demo_01) == "+"])
reverse <- end(reads_demo_01[strand(reads_demo_01) == "-"])

## Run nucleosome positioning
result <- RJMCMCNucleosomes:::rjmcmcNucleo(
            startPosForwardReads = forward,
            startPosReverseReads = reverse,
            nbrIterations = 1000, lambda = 2, kMax = 30,
            minInterval = 146, maxInterval = 292, minReads = 5,
            adaptIterationsToReads = TRUE, vSeed = -1)

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

## Print the position of nucleosomes
result$mu

RJMCMCNucleosomes documentation built on Nov. 8, 2020, 8:20 p.m.