CopyEstimate

CopyEstimate-class

CopyEstimate,GRanges,matrix,GRangesList,character-method

show,CopyEstimate-method


  Contains the genomic coordinates of regions, and fold change estimates.


Tools for the analysis of enrichment-based epigenomic
data.  Features include summarization and visualization of
epigenomic data across promoters according to gene expression
context, finding regions of differential methylation/binding,
BayMeth for quantifying methylation etc.

Mark Robinson

Repitools

Epigenomic tools

CopyEstimate function

<dl>
    <dt></dt><dd>
    	<code>CopyEstimate(windows, unadj.CN, unadj.CN.seg)</code>
	Creates a CopyEstimate object.
	<dl>
	    <dt><code>windows</code></dt><dd>A <code>GRanges</code> object.</dd> <dt><code>unadj.CN</code></dt><dd>A matrix of fold changes.</dd> <dt><code>unadj.CN.seg</code></dt><dd>A <code>GRangesList</code> object holding
                                       the segmentation results.</dd> </dl> </dd> </dl> 

Constructor

<dl>
      These are added to by <code><a rd-options="" href="/link/absoluteCN?package=Repitools&version=1.18.0" data-mini-rdoc="Repitools::absoluteCN">absoluteCN</a></code> or <code><a rd-options="" href="/link/relativeCN?package=Repitools&version=1.18.0" data-mini-rdoc="Repitools::relativeCN">relativeCN</a></code>
    <dt>type</dt><dd>A flag that contains if the copy number data is absolute or relative.</dd> </dl> 

Additional Slots

Contains the genomic coordinates of regions, and fold change estimates.

CopyEstimate: Container for results of fold change copy number estimation.

Description

Arguments

Constructor

Additional Slots