plotSummary {PING} | R Documentation

## Plot a summary of the prediction for given ranges.

### Description

This function use Gviz package to summarize the nucleosome position prediction from postPING.

### Usage

    plotSummary(PS, ping, reads, chr, gen="gen", from=NULL, to=NULL, FragmentLength=200, title="", scoreThreshold=0.05)

### Arguments

`PS` | A `data.frame`. The output `postPING`. If a list of `data.frame` is passed, multiple `NucleosomeTrack` will be plotted.
`ping` | A `pingList`. The output of `PING`.
`reads` | A `GRanges` object. The reads used in the segmentation process.
`chr` | A character string for the chromosome name.
`gen` | An optional character string for the genome name.
`from` | An `integer`, the first base of the plot
`to` | An `integer`, the last base of the plot
`FragmentLength` | An `integer`, the length of XSET profile extension in the `CoverageTrack`. This argument will be ignored if the reads are paired-end sequencing data.

`title` | An optional character string that can be prepend to the automatically generated title.
`scoreThreshold` | A `numeric`. Removes nucleosome with a score inferior to the threshold from the plot.

### Value

This function returns an invisible `list` of tracks. The tracks can be used in other Gviz plots.

### Author(s)

Renan Sauteraud

### See Also

`CoverageTrack` `RawReadsTrack` `NucleosomeTrack` `plotTracks`

[Package PING version 2.30.0 Index]