plotNucleosomes {RJMCMCNucleosomes} | R Documentation |
Generate a graph of nucleosome positions with read coverage
Description
Generate a graph for
a GRanges
or a GRangesList
of nucleosome positions. In
presence of only one prediction (with multiples nucleosome positions), a
GRanges
is used. In presence of more thant one predictions (as
example, before and after post-treatment or results from
different software), a GRangesList
with
one entry per prediction is used. All predictions must have been obtained
using the same reads.
Usage
plotNucleosomes(nucleosomePositions, reads, seqName = NULL,
xlab = "position", ylab = "coverage", names = NULL)
Arguments
nucleosomePositions |
a GRanges or a GRangesList
containing the nucleosome positions for one or
multiples predictions obtained using the same reads. In presence of
only one prediction (with multiples nucleosome positions), a GRanges
is used. In presence of more thant one predictions (as example, before and
after post-treatment or results from different software), a
GRangesList with one entry per prediction is used.
|
reads |
a GRanges containing forward and
reverse reads. The GRanges should contain at least one read.
|
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 .
|
xlab |
a character string containing the label of the x-axis.
|
ylab |
a character string containing the label of the y-axis.
|
names |
a vector of a character string containing the
label of each prediction set. The vector must be the same length of
the nucleosomePositions list or 1 in presence of a
vector . When NULL , the name of the elements of the list
are used or the string "Nucleosome" for a vector are used.
Default: NULL .
|
Value
a graph containing the nucleosome positions and the read coverage
Author(s)
Astrid Deschenes
Examples
## Load reads dataset
data(reads_demo_01)
## Run RJMCMC method
result <- rjmcmc(reads = reads_demo_01,
seqName = "chr_SYNTHETIC",
nbrIterations = 4000, lambda = 2, kMax = 30,
minInterval = 146, maxInterval = 292, minReads = 5,
vSeed = 10213)
## Create graph using the synthetic map
plotNucleosomes(nucleosomePositions = result$mu, seqName = "chr_SYNTHETIC",
reads = reads_demo_01)
[Package
RJMCMCNucleosomes version 1.4.0
Index]