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

Description Usage Arguments Details Value Note Author(s) References Examples

Returns a ggplot2 plot object representing a matrix of significant features. This is a useful synopsis of all significant pairwise comparisons within the dataset.

1 2	## S4 method for signature 'CuffSet' sigMatrix(object,alpha=0.05,level='genes',orderByDist=FALSE)

`object`	An object of class CuffSet.
`alpha`	An alpha value by which to filter multiple-testing corrected q-values to determine significance
`level`	Feature level to be queried for significance (must be one of c('genes','isoforms','TSS','CDS')
`orderByDist`	Logical. If TRUE then samples are re-ordered based on JS-distance from one another (fairly useless unless you have a specific need for this).

Creates a matrix plot to illustrate the number of significant features of type 'level' at a given alpha from a cuffdiff run.

A ggplot2 plot object

None

Loyal A. Goff

None

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	a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data
	d<-sigMatrix(a) #Create csDensity plot
	d #Render plot