csDendro: csDendro

In cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

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)

cummeRbund documentation built on Nov. 8, 2020, 7:53 p.m.