report,Eigensystem,EigensystemPlotParam-method {biosvd} | R Documentation |
Generates a summarizing report of the eigensystem
## S4 method for signature 'Eigensystem,EigensystemPlotParam' report(x, y, ...)
x |
object of class Eigensystem |
y |
object of class EigensystemPlotParam |
... |
Additional arguments that can be passed on |
The function generates a txt file of the eigensystem, containing the list of features with their coordinates, radius and phase in the polar plot according to two selected eigenfeatures.
signature(x = "Eigensystem", y = "EigensystemPlotParam")
Anneleen Daemen daemen.anneleen@gene.com, Matthew Brauer brauer.matthew@gene.com
Other X.eigensystem.: compute
,
compute,Eigensystem-method
,
compute,ExpressionSet-method
,
compute,data.frame-method
,
compute,matrix-method
;
exclude
,
exclude,Eigensystem-method
;
plot
,
plot,Eigensystem,EigensystemPlotParam-method
## 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) ## Exclude the eigenfeatures representing steady-state intensity eigensystem <- exclude(eigensystem) ## Computes the eigensystem on the variance in the data after filtering out stead-state intensity eigensystem <- compute(eigensystem, apply="variance") ## No exclusion of eigenfeatures representing steady-scale variance eigensystem <- exclude(eigensystem, excludeEigenfeatures=0) ## Generate report for eigenfeatures 1 and 2 params <- new("EigensystemPlotParam") if (.Platform$OS.type %in% "windows") path(params) <- getwd() report(eigensystem, params) ## Generate report for eigenfeatures 2 and 3 whichPolarAxes(params) <- c(3,2) report(eigensystem, params)