project,Eigensystem-method {biosvd} | R Documentation |
Returns the rectangular and polar coordinates of the eigensystem projection onto one or two eigenfeatures and eigenassays
## S4 method for signature 'Eigensystem' project(x, axes = c(2, 1), type = "features")
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) |
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.
data.frame
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).
## 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))