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cummeRbund (version 2.14.0)

sigMatrix: sigMatrix

Description

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

Usage

"sigMatrix"(object,alpha=0.05,level='genes',orderByDist=FALSE)

Arguments

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).

Value

A ggplot2 plot object

Details

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

References

None

Examples

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

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