csDendro {cummeRbund} | R Documentation

## csDendro

### Description

Creates a grid graphics plot of a dendrogram of Jensen-Shannon distances between conditions of a CuffFeatureSet or CuffGeneSet object.

### Usage

    ## S4 method for signature 'CuffFeatureSet'
    csDendro(object,logMode=T,pseudocount=1,replicates=FALSE)
    ## S4 method for signature 'CuffData'
    csDendro(object,logMode=T,pseudocount=1,replicates=FALSE,...)

### Arguments

`object` | An object of class 'CuffFeatureSet' or 'CuffGeneSet'
`logMode` | A logical argument to log10-transform FPKM values prior to plotting.
`pseudocount` | Value to be added to FPKM for appropriate log transformation and clustering. (Avoids zero-based errors)
`replicates` | A logical value whether or not to plot individual replicates or aggregate condition values.
`...` | Additional arguments to csHeatmap

### Details

None

### Value

Returns a dendrogram object and plots that object by default.

### Note

None

### Author(s)

Loyal A. Goff and Cole Trapnell

### References

None.

### Examples

    	data(sampleData)
    	csDendro(sampleGeneSet)

[Package cummeRbund version 2.28.0 Index]