biosvd (version 2.8.0)

project,Eigensystem-method: Projects the data onto one or two eigenfeatures and eigenassays

Description

Returns the rectangular and polar coordinates of the eigensystem projection onto one or two eigenfeatures and eigenassays

Usage

"project"(x, axes = c(2, 1), type = "features")

Arguments

x

object of class Eigensystem

axes

numerical vector specifying eigenfeatures to project onto (default c(2,1))

type

string specifying the dimensions to return the coordinates for, either features or assays (default features)

Value

data.frame

Methods

signature(x = "Eigensystem")

Details

The function allows the sorting of the data according to one or two specified eigenfeatures and eigenassays. This gives a global picture of the dynamics of expression/intensities, in which individual features and assays are classified in groups of similar regulation and function or similar cellular state and biological phenotype.

References

Alter O, Brown PO and Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U.S.A. 97(18), 10101-10106 (2000).

Examples

## Data obtained from http://genomics-pubs.princeton.edu/StarvationMetabolomics/Download.shtm
data(StarvationData)

## Computes the eigensystem for the actual data
eigensystem <- compute(StarvationData)
## Excludes the eigenfeatures representing steady-state intensity
eigensystem <- exclude(eigensystem)

## Find the projection of the data onto eigenfeature 1 and 2
projection <- project(eigensystem)
## Project the data onto eigenfeature 3 and 4
projection <- project(eigensystem, axes=c(4,3))