MappedRead-class

show,MappedRead-method

drawGD,MappedRead-method

datasets

Genomic data analyses requires integrated visualization of known genomic information and new experimental data.  GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.  Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system.

Steffen Durinck

GenomeGraphs

Plotting genomic information from Ensembl

MappedRead-class function

<dl>
    <dt><code>start</code>:</dt><dd>Object of class <code>"numeric"</code>, containing start position of the reads</dd> <dt><code>end</code>:</dt><dd>Object of class <code>"numeric"</code>, containing end position of the reads</dd> <dt><code>strand</code>:</dt><dd>Object of class <code>"numeric"</code>, containing strand  to which the reads map</dd> <dt><code>chromosome</code>:</dt><dd>Object of class <code>"numeric"</code>, containing chromosome to which the reads map</dd> </dl> 

Slots

<dl>
    <dt>show</dt><dd><code>signature(object = "MappedRead")</code>: ... </dd> </dl> 

MappedRead-class: Represents mapped reads

Description

Arguments

Slots

Methods

References

Examples