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)

- ibterms
`signature(object = "NMF")`

: Default pure virtual method that ensure a method is defined for concrete NMF model classes. - ibterms
`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. - ibterms
`signature(object = "NMFfit")`

: Method for single NMF fit objects, which returns the indexes of fixed basis terms from the fitted model. - ibterms
`signature(object = "NMFfitX")`

: Method for multiple NMF fit objects, which returns the indexes of fixed basis terms from the best fitted model. - icterms
`signature(object = "NMF")`

: Default pure virtual method that ensure a method is defined for concrete NMF model classes. - icterms
`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. - icterms
`signature(object = "NMFfit")`

: Method for single NMF fit objects, which returns the indexes of fixed coefficient terms from the fitted model.