postMerge: A internal post treatment function to merge closely...

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

Description

A internal helper function which merges closely positioned nucleosomes to rectify the over splitting and provide a more conservative approach. Beware that each chromosome must be treated separatly.

The function uses the Bioconductor package consensusSeeker to group closely positioned nucleosomes.

Usage

postMerge(reads, resultRJMCMC, extendingSize, chrLength, minReads = 5,
  seqName = NULL)

Arguments

reads	a GRanges containing all forward and reverse reads.The start positions of both reads are going to be used for the analysis. Beware that the start position of a reverse read is always higher that the end positition.
resultRJMCMC	an object of class 'rjmcmcNucleosomes' or 'rjmcmcNucleosomesMerge' containing informations about nucleosomes.
extendingSize	a positive numeric or a positive integer indicating the size of the consensus region used to group closeley positioned nucleosomes.The minimum size of the consensus region is equal to twice the value of the extendingSize parameter. The numeric will be treated as an integer.
chrLength	a positive numeric or a positive integer indicating the lenght of the current chromosome. The length of the chromosome is used to ensure that the consensus positions are all located inside the chromosome.
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.

Value

a array of numeric, the updated values of the nucleosome positions. When no nucleosome is present, NULL is returned.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

## Loading dataset
data(RJMCMC_result)
data(reads_demo_02)

## Results before post-treatment
RJMCMC_result$mu

## Post-treatment function which merged closely positioned nucleosomes
postResult <- RJMCMCNucleosomes:::postMerge(reads = reads_demo_02,
resultRJMCMC = RJMCMC_result, extendingSize = 80, chrLength = 73500)

## Results after post-treatment
postResult

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