cummeRbund (version 2.14.0)

Dimensionality Reduction: Dimensionality reduction utilities

Description

Dimensionality reduction plots for feature selection and extraction for cummeRbund

Usage

"MDSplot"(object,replicates=FALSE,logMode=TRUE,pseudocount=1.0)
"PCAplot"(object,x="PC1", y="PC2",replicates=FALSE,pseudocount=1.0,scale=TRUE,showPoints = TRUE,...)

Arguments

object

The output of class CuffData from which to draw expression estimates. (e.g. genes(cuff))

x

For PCAplot, indicates which principal component is to be presented on the x-axis (e.g. "PC1","PC2","PC3", etc)

y

See x.

pseudocount

Value added to FPKM to avoid log transformation issues.

logMode

Logical value whether or not to use log-transformed expression estimates (default: TRUE)

replicates

A logical value to indicate whether or not individual replicate expression estimates will be used.

scale

For PCAplot, a logical value passed directly to prcomp.

showPoints

For PCAplot, a logical value whether or not to display individual gene values on final PCA plot.

...

Additional passthrough arguments (may not be fully implemented yet).

Value

A ggplot2 object.

Details

These methods attempt to project a matrix of expression estimates across conditions and/or replicates onto a smaller number of dimesions for feature selection, feature extraction, and can also be useful for outlier detection.

References

None.

Examples

	cuff<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data
	p<-PCAplot(genes(cuff),x="PC2",y="PC3",replicates=TRUE)
	m<-MDSplot(genes(cuff),replicates=TRUE)
	p #Render PCA plot
	m #Render MDS plot