sigMatrix: sigMatrix

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

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

gofflab/cummeRbund-BioC-Bridge documentation built on May 17, 2019, 7:30 a.m.