syntheticNucMap {nucleR} | R Documentation

## Generates a synthetic nucleosome map

### Description

This function generates a synthetic nucleosome map using the parameters given by the user and returns the coverage (like NGS experiments) or a pseudo-hybdridization ratio (like Tiling Arrays) toghether with the perfect information about the well positioned and fuzzy nucleosome positions.

### Usage

    syntheticNucMap(wp.num = 100, wp.del = 10, wp.var = 20, fuz.num = 50,
      fuz.var = 50, max.cover = 20, nuc.len = 147, lin.len = 20,
      rnd.seed = NULL, as.ratio = FALSE, show.plot = FALSE)

### Arguments

`wp.num` | Number of well-positioned (non overlapped) nucleosomes. They are placed uniformly every `nuc.len+lin.len` basepairs.
`wp.del` | Number of well-positioned nucleosomes (the ones generated by `wp.num`) to remove. This will create an uncovered region.
`wp.var` | Maximum variance in basepairs of the well-positioned nucleosomes. This will create some variation in the position of the reads describing the same nucleosome.
`fuz.num` | Number of fuzzy nucleosomes. They are distributed randomly over all the region. They could be overlapped with other well-positioned or fuzzy nucleosomes.
`fuz.var` | Maximum variance of the fuzzy nucleosomes. This allow to set different variance in well-positioned and fuzzy nucleosome reads (using `wp.var` and `fuz.var`).
`max.cover` | Maximum coverage of a nucleosome, i.e., how many times a nucleosome read can be repeated. The final coverage probably will be higher by the addition of overlapping nucleosomes.
`nuc.len` | Nucleosome length. It's not recomended change the default 147bp value.
`lin.len` | Linker DNA length. Usually around 20 bp.
`rnd.seed` | As this model uses random distributions for the placement, by setting the rnd.seed to a known value allows to reproduce maps in different executions or computers. If you don't need this, just left it in default value.
`as.ratio` | If `as.ratio=TRUE` this will create and return a synthetic naked DNA control map and the ratio between it and the nucleosome coverage. This can be used to simulate hybridization ratio data, like the one in Tiling Arrays.
`show.plot` | If `TRUE`, will plot the output coverage map, with the nucleosome calls and optionally the calculated ratio.

### Value

A list with the following elements:

- wp.starts Start points of well-positioned nucleosomes

- wp.nreads Number of repetitions of each well positioned read

- wp.reads Well positioned nucleosome reads (`IRanges` format), containing the repetitions

- fuz.starts Start points of the fuzzy nucleosomes

- fuz.nreads Number of repetitions of each fuzzy nucleosome read

- fuz.reads Fuzzy nucleosome reads (`IRanges` format), containing all the repetitions

- syn.reads All synthetic nucleosome reads togheter (`IRanges` format)

The following elements will be only returned if `as.ratio=TRUE`:

- ctr.reads The pseudo-naked DNA (control) reads (`IRanges` format)

- syn.ratio The calculated ratio nucleosomal/control (`Rle` format)

### Author(s)

Oscar Flores oflores@mmb.pcb.ub.es

### Examples

    # Generate a synthetic map with 50wp + 20fuzzy nucleosomes using fixed
    # random seed=1
    res <- syntheticNucMap(wp.num=50, fuz.num=20, show.plot=TRUE, rnd.seed=1)

    # Increase the fuzzyness
    res <- syntheticNucMap(
        wp.num=50, fuz.num=20, wp.var=70, fuz.var=150, show.plot=TRUE,
        rnd.seed=1
    )

    # Calculate also a random map and get the ratio between random and
    # nucleosomal
    res <- syntheticNucMap(
        wp.num=50, wp.del=0, fuz.num=20, as.ratio=TRUE, show.plot=TRUE,
        rnd.seed=1
    )

    print(res)

    # Different reads can be accessed separately from results
    # Let's use this to plot the nucleosomal + the random map
    library(ggplot2)
    as <- as.vector(coverage.rpm(res$syn.reads))
    bs <- as.vector(coverage.rpm(res$ctr.reads))
    cs <- as.vector(res$syn.ratio)
    plot_data <- rbind(
        data.frame(x=seq_along(as), y=as, lab="nucleosomal"),
        data.frame(x=seq_along(bs), y=bs, lab="random"),
        data.frame(x=seq_along(cs), y=cs, lab="ratio")
    )
    qplot(x=x, y=y, data=plot_data, geom="area", xlab="position", ylab="") +
        facet_grid(lab~., scales="free_y")

[Package nucleR version 2.12.1 Index]