plot.cher

plotCher

cherPlot

plot,cher,missing-method

plot,cher,ExpressionSet-method

data object of class <code>ExpressionSet</code> that was used for
    function <code>findChersOnSmoothed</code>

object of class <code>probeAnno</code>
    holding the reporter/probe to genome mappings

probeAnno

which samples to plot, either a numeric vector of
    entries in 1 to <code>ncol(dat)</code>, or character vector with entries
    in <code>sampleNames(dat)</code> or <code>NULL</code> meaning plot the levels
    from all samples in the ExpressionSet

samples

integer; how many base pairs to the left and right
    should the plotted genomic region be extended

extent

data frame with gene/transcript annotation

further arguments passed on to function
    <code>chipAlongChrom</code>


  Function for plotting identified <em>Cher</em>s (ChIP-enriched regions).


hplot

The package Ringo facilitates the primary analysis
of ChIP-chip data. The main functionalities of the package are
data read-in, quality assessment, data visualisation and
identification of genomic regions showing enrichment in ChIP-chip.
The package has functions to deal with two-color oligonucleotide
microarrays from NimbleGen used in ChIP-chip projects, but also
contains more general functions for ChIP-chip data analysis, given
that the data is supplied as RGList (raw)  or ExpressionSet (pre-
processed).
The package employs functions from various other packages of the
Bioconductor project and provides additional ChIP-chip-specific
and NimbleGen-specific functionalities.

plot.cher: Plot identified Chers

Description

Usage

Arguments

Value

See Also