csDendro

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Description

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

Usage

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## 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

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	data(sampleData)
	csDendro(sampleGeneSet)

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