MAplot: MAplot

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

View source: R/methods-CuffData.R

Description

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

Usage

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## 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

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	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

cummeRbund documentation built on May 2, 2018, 3:12 a.m.