csAnno-class

plotAnnoBar,csAnno-method

plotAnnoPie,csAnno-method

plotDistToTSS,csAnno-method

show,csAnno-method

upsetplot,csAnno-method

vennpie,csAnno-method


Class "csAnno"
This class represents the output of ChIPseeker Annotation


classes

This package implements functions to retrieve the nearest genes
around the peak, annotate genomic region of the peak, statstical methods
for estimate the significance of overlap among ChIP peak data sets, and
incorporate GEO database for user to compare the own dataset with those
deposited in database. The comparison can be used to infer cooperative
regulation and thus can be used to generate hypotheses. Several
visualization functions are implemented to summarize the coverage of the
peak experiment, average profile and heatmap of peaks binding to TSS
regions, genomic annotation, distance to TSS, and overlap of peaks or
genes.

Guangchuang Yu

ChIPseeker

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

csAnno-class function

 <dl>
<dt><code>anno</code></dt><dd>annotation</dd> <dt><code>tssRegion</code></dt><dd>TSS region</dd> <dt><code>level</code></dt><dd>transcript or gene</dd> <dt><code>hasGenomicAnnotation</code></dt><dd>logical</dd> <dt><code>detailGenomicAnnotation</code></dt><dd>Genomic Annotation in detail</dd> <dt><code>annoStat</code></dt><dd>annotation statistics</dd> <dt><code>peakNum</code></dt><dd>number of peaks</dd> </dl>

Slots

Class "csAnno"
This class represents the output of ChIPseeker Annotation

csAnno-class: Class "csAnno" This class represents the output of ChIPseeker Annotation

Description

Arguments

Slots

See Also