R: Generate a graph of nucleosome positions with read coverage

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]