MAplot: MAplot

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

Description

Creates an M vs A plot (Avg intensity vs log ratio) for a given pair of conditions across all fpkms

Usage

## S4 method for signature 'CuffData'
MAplot(object,x,y,logMode=T,pseudocount=1,smooth=FALSE,useCount=FALSE)

Arguments

object	An object of class 'CuffData'.
x	Sample name from 'samples' table for comparison
y	Sample name from 'samples' table for comparison
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)
smooth	Logical argument whether or not to draw a smoothed line fit through data.
useCount	Logical argument whether or not to use mean counts instead of FPKM values.

Details

None

Value

Returns a ggplot MvsA plot object.

Note

None

Author(s)

Loyal A. Goff and Cole Trapnell

References

None.

Examples

	a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data
	genes<-a@genes #Create CuffData object for all 'genes'
	d<-MAplot(genes,'hESC','Fibroblasts') #Create csDensity plot
	d #Render plot

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