Description Usage Arguments Details Value Methods Author(s) References See Also Examples
Excludes specified eigenfeatures/eigenassays from the original data
1 2 | ## S4 method for signature 'Eigensystem'
exclude(x, excludeEigenfeatures = NULL)
|
x |
object of class eigensystem |
excludeEigenfeatures |
vector of positive integers representing eigenfeatures to be excluded from the data |
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).
Object of class eigensystem
signature(x = "Eigensystem")
Anneleen Daemen daemen.anneleen@gene.com, Matthew Brauer brauer.matthew@gene.com
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).
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## 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)
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