plotNucleosomes: Generate a graph of nucleosome positions with read coverage

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

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)

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