dimensionality: Dimensionality reduction utilities

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

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
	

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