project-methods: Projects the data onto one or two eigenfeatures and...

In biosvd: Package for high-throughput data processing, outlier detection, noise removal and dynamic modeling

Description

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

Usage

## S4 method for signature 'Eigensystem'
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)

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.

Value

data.frame

Methods

signature(x = "Eigensystem")

Author(s)

Anneleen Daemen [e-mail], Matthew Brauer [e-mail]

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))

biosvd documentation built on April 28, 2020, 6:32 p.m.