priorMuDensity: Prior density of mu

In ArnaudDroitLab/RJMCMC: Bayesian hierarchical model for genome-wide profiling of nucleosome positions based on high-throughput short-read data (MNase-Seq data)

Description

Computes the prior density of mu conditionally to the number of nucleosomes.

For more information on the calculation of the prior density of mu, see Proposotion 1 and equation (11) of the cited article.

Usage

priorMuDensity(mu, readPositions)

Arguments

mu	a vector of positive integer containing the positions of all nucleosomes.
readPositions	a vector of positive integer corresponding to the positions of all reads, including forward and reverse strands. The values insinde readPositions must be sorted.

Value

a numeric, the exact prior density of mu given the number of nucleosomes.

Author(s)

Rawane Samb, Astrid Deschenes

References

Samb R., Khadraoui K., Belleau P., Deschenes A., Lakhal L. and Droit A. Using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling. Statistical Applications in Genetics and Molecular Biology. Volume 14, Issue 6, Pages 517-532, ISSN (Online) 1544-6115, ISSN (Print) 2194-6302, DOI: 10.1515/sagmb-2014-0098, December 2015

Examples

## Sorted vector of read positions, including forward and reverse
readPositions <- c(9909L, 9928L, 9935L, 26603L, 26616L, 26632L, 26636L,
26640L, 44900L, 44902L, 44909L,  44910L, 44910L, 44918L,
44924L, 44931L, 44935L, 44942L, 44946L)

## Position of the group of nucleosomes
mu <- c(10000L, 26700L, 45000L)

## Calculation of the exact prior density of mu
density <- RJMCMC:::priorMuDensity(mu, readPositions)

ArnaudDroitLab/RJMCMC documentation built on May 5, 2019, 7:06 a.m.