Description Details Slots Accessors Author(s) References See Also Examples
Eigensystem
is a list-based class for storing the results of applying Singular Value Decomposition (SVD) to a feature by assay data set. Objects are normally created by compute,Eigensystem-method
.
The Eigensystem
class stores the original data and all SVD-derived information obtained with compute
.
Data in the Eigensystem
are organized into different slots,
‘matrix’, ‘signMatrix’, ‘assayMatrix’, ‘featureMatrix’,
‘eigenassays’, ‘eigenexpressions’, ‘eigenfeatures’,
‘assaycorrelations’, ‘featurecorrelations’, ‘fractions’,
‘entropy’, ‘apply’, ‘excludeEigenfeatures’, and ‘colorIdFeatures’.
Brief descriptions of these slots are provided below.
Eigensystem
objects contain the following slots
matrix
:matrix
containing the feature by assay data without missing values
signMatrix
:matrix
containing the sign of each element in matrix
assayMatrix
:matrix
containing additional information about assays, with rows as assays and columns as additional variables
featureMatrix
:matrix
containing additional information about features, with rows as features and columns as additional variables
eigenassays
:matrix
containing the feature by eigenassay data, with each column in eigenassays corresponding to a left singular vector, representing genome-wide expression, proteome-wide abundance or metabolome-wide intensity in the corresponding eigenassay
eigenexpressions
:numeric
vector containing the eigenexpression fraction of each eigenfeature, eigenassay-pair, constituting the diagonal elements of the diagonal matrix connecting the left and right singular values; the diagonal matrix reflects the decoupling and decorrelation of the data, with expression of each eigenfeature restricted to the corresponding eigenassay
eigenfeatures
:matrix
containing the eigenfeatures by assay data, with each row corresponding to a right singular vector, representing the expression, abundance or intensity of the corresponding eigenfeature across all assays
assaycorrelations
:matrix
containing the correlation between the eigenassays as rows and the assays as columns
featurecorrelations
:matrix
containing the correlation between the eigenfeatures as rows and features as columns
fractions
:numeric
vector containing the eigenexpression fraction for each eigenfeature, eigenassay-pair, defined as the relative fraction of overall expression that each eigenfeature and eigenassay capture
entropy
:numeric
value between 0 and 1 giving the Shannon entropy as measure for data complexity, with an entropy of 0 corresponding to an ordered and redundant data set with all expression captured by a single eigenfeature, eigenassay-pair, and an entropy of 1 corresponding to a disordered and random data set with all eigenfeature, eigenassay-pairs equally expressed
apply
:character
containing whether the eigensystem should be computed for the actual data or the variance in the data
excludeEigenfeatures
:numeric
vector containing eigenfeature 1 and 2 in case they capture >85% of the data with eigenfeature 2 capturing at least 15%, otherwise numeric value containing eigenfeature 1
colorIdFeatures
:numeric
vector or factor
containing annotation information on the features
matrix(x)
, matrix(x) <- value
signMatrix(x)
, signMatrix(x) <- value
assayMatrix(x)
, assayMatrix(x) <- value
featureMatrix(x)
, featureMatrix(x) <- value
eigenassays(x)
, eigenassays(x) <- value
eigenexpressions(x)
, eigenexpressions(x) <- value
eigenfeatures(x)
, eigenfeatures(x) <- value
assaycorrelations(x)
, assaycorrelations(x) <- value
featurecorrelations(x)
, featurecorrelations(x) <- value
fractions(x)
, fractions(x) <- value
entropy(x)
, entropy(x) <- value
apply(x)
, apply(x) <- value
excludeEigenfeatures(x)
, excludeEigenfeatures(x) <- value
colorIdFeatures(x)
, colorIdFeatures(x) <- value
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).
compute,Eigensystem-method
1 2 3 4 5 6 7 8 | ## Metabolomics starvation data obtained from http://genomics-pubs.princeton.edu/StarvationMetabolomics/Download.shtml
data(StarvationData)
## An object from class Eigensystem is obtained with the compute method
eigensystem <- compute(StarvationData)
## Obtain entropy
entropy(eigensystem)
|
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