postTreatment: A post-treatment function to merge closely positioned...

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

Description

A 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.

Usage

postTreatment(reads, seqName = NULL, resultRJMCMC, extendingSize = 74L,
  chrLength)

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.
resultRJMCMC	an object of class "rjmcmcNucleosomes" or "rjmcmcNucleosomesMerge", the information about nucleosome positioning for an entire chromosome or a region that must be treated as one unit.
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. Default: 74.
chrLength	a positive numeric or a positive integer indicating the length of the current chromosome. The length of the chromosome is used to ensure that the consensus positions are all located inside the chromosome.

Value

a GRanges, the updated nucleosome positions. When no nucleosome is present, NULL is returned.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

## Loading dataset
data(reads_demo_02)

## Nucleosome positioning, running both merge and split functions
result <- rjmcmc(reads = reads_demo_02,
            seqName = "chr_SYNTHETIC", nbrIterations = 1000,
            lambda = 2, kMax = 30, minInterval = 146,
            maxInterval = 490, minReads = 3, vSeed = 11)

## Before post-treatment
result

##Post-treatment function which merged closely positioned nucleosomes
postResult <- postTreatment(reads = reads_demo_02,
                    seqName = "chr_SYNTHETIC", result, 100, 73500)

## After post-treatment
postResult

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