biosvd (version 2.8.0)

exclude,Eigensystem-method: Excludes specified eigenfeatures/eigenassays from the data

Description

Excludes specified eigenfeatures/eigenassays from the original data

Usage

"exclude"(x, excludeEigenfeatures = NULL)

Arguments

x

object of class eigensystem

excludeEigenfeatures

vector of positive integers representing eigenfeatures to be excluded from the data

Value

Object of class eigensystem

Methods

signature(x = "Eigensystem")

Details

The function excludes eigenfeatures/eigenassays from the data that correspond to steady-state intensity, steady-scale variance, experimental artifacts and/or noise as specified by the user. In case no eigenfeatures are specified, the eigenfeature(s) corresponding to steady-state/steady-scale is/are removed. Filtering out steady-state expression/intensity corresponds to centering the expression/intensity patterns at steady-state expression/intensity level (arithmetic mean of expression/intensity ~ 0). Filtering out steady-scale variance corresponds to normalization by the steady scale of expression/intensity variance (geometric mean of variance ~ 1).

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).

See Also

Other X.eigensystem.: compute, compute,Eigensystem-method, compute,ExpressionSet-method, compute,data.frame-method, compute,matrix-method; plot, plot,Eigensystem,EigensystemPlotParam-method; report, report,Eigensystem,EigensystemPlotParam-method

Examples

## Metabolomics starvation data obtained from http://genomics-pubs.princeton.edu/StarvationMetabolomics/Download.shtml
data(StarvationData)

## Computes the eigensystem for the actual data
eigensystem <- compute(StarvationData)
## Excludes the eigenfeature(s) representing steady-state expression/intensity as defined in compute
exclude(eigensystem)
## Excludes user-specified eigenfeatures 1, 4 and 5
exclude(eigensystem, excludeEigenfeatures=c(1,4,5))

## Computes the eigensystem for the variance in the data
eigensystem <- compute(StarvationData, apply="variance")
## Excludes the eigenfeature(s) representing steady-scale variance as defined in compute
eigensystem <- exclude(eigensystem)
## Excludes none of the eigenfeatures and recalculates the eigensystem for the actual data
eigensystem <- exclude(eigensystem, excludeEigenfeatures=0)