R: Fixed Terms in NMF Models

ibterms {NMF} | R Documentation

## Fixed Terms in NMF Models

### Description

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.

### Usage

      ibterms(object, ...)

      icterms(object, ...)

      iterms(object, ...)

      nterms(object)

      nbterms(object)

      ncterms(object)

      bterms(object)

      cterms(object)

      ibasis(object, ...)

      icoef(object, ...)

### Arguments

`object` | NMF object
`...` | extra parameters to allow extension (currently not used)

### Methods

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.

[Package NMF version 0.21.0 Index]