Plot a summary of the prediction for given ranges.

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Description

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

Usage

1
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