sigMatrix {cummeRbund} | R Documentation

## 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

    ## S4 method for signature 'CuffSet'
    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).

### Details

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

### Value

A ggplot2 plot object

### Note

None

### Author(s)

Loyal A. Goff

### References

None

### Examples

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

[Package cummeRbund version 2.28.0 Index]