postTreatment {RJMCMCNucleosomes} | R Documentation |
A post-treatment function to merge closely positioned nucleosomes,
from the same chromosome, identified by the rjmcmc
function.
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
[Package
RJMCMCNucleosomes version 1.16.0
Index]