Dimensionality Reduction {cummeRbund} | R Documentation

## Dimensionality reduction utilities

### Description

Dimensionality reduction plots for feature selection and extraction for cummeRbund

### Usage

    ## S4 method for signature 'CuffData'
    MDSplot(object,replicates=FALSE,logMode=TRUE,pseudocount=1.0)
    ## S4 method for signature 'CuffData'
    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).

### 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.

### Value

A ggplot2 object.

### Note

None.

### Author(s)

Loyal A. Goff

### 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

[Package cummeRbund version 2.28.0 Index]