Fixed Terms in NMF Models
Formula-based NMF models may contain fixed basis and/or
coefficient terms. The functions documented here provide
access to these data, which are read-only and defined
when the model object is instantiated (e.g., see
nmfModel,formula-method).
ibterms, icterms and iterms
respectively return the indexes of the fixed basis terms,
the fixed coefficient terms and all fixed terms, within
the basis and/or coefficient matrix of an NMF model.
nterms, nbterms, and ncterms return,
respectively, the number of all fixed terms, fixed basis
terms and fixed coefficient terms in an NMF model. In
particular: i.e. nterms(object) = nbterms(object) +
ncterms(object).
bterms and cterms return, respectively, the
primary data for fixed basis and coefficient terms in an
NMF model – as stored in slots bterms and
cterms . These are factors or numeric vectors
which define fixed basis components, e.g., used for
defining separate offsets for different a priori
groups of samples, or to incorporate/correct for some
known covariate.
ibasis and icoef return, respectively, the
indexes of all latent basis vectors and estimated
coefficients within the basis or coefficient matrix of an
NMF model.
ibterms(object, ...) icterms(object, ...) iterms(object, ...) nterms(object) nbterms(object) ncterms(object) bterms(object) cterms(object) ibasis(object, ...) icoef(object, ...)
object |
NMF object |
... |
extra parameters to allow extension (currently not used) |
signature(object = "NMF"): Default
pure virtual method that ensure a method is defined for
concrete NMF model classes.
signature(object = "NMFstd"):
Method for standard NMF models, which returns the integer
vector that is stored in slot ibterms when a
formula-based NMF model is instantiated.
signature(object = "NMFfit"):
Method for single NMF fit objects, which returns the
indexes of fixed basis terms from the fitted model.
signature(object = "NMFfitX"):
Method for multiple NMF fit objects, which returns the
indexes of fixed basis terms from the best fitted model.
signature(object = "NMF"): Default
pure virtual method that ensure a method is defined for
concrete NMF model classes.
signature(object = "NMFstd"):
Method for standard NMF models, which returns the integer
vector that is stored in slot icterms when a
formula-based NMF model is instantiated.
signature(object = "NMFfit"):
Method for single NMF fit objects, which returns the
indexes of fixed coefficient terms from the fitted model.
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