NMF 0.17.4

Sub-setting NMF Objects

Description

This method provides a convenient way of sub-setting objects of class NMF, using a matrix-like syntax.

Usage

S4 (NMF)
`[`(x, i, j, ..., drop = FALSE)

Arguments

i
index used to subset on the rows of the basis matrix (i.e. the features). It can be a numeric, logical, or character vector (whose elements must match the row names of x). In the case of a logical vector the entries are recycled if necessary.
j
index used to subset on the columns of the mixture coefficient matrix (i.e. the samples). It can be a numeric, logical, or character vector (whose elements must match the column names of x). In the case of a logical vector the entries are recycled if necessary.
...
used to specify a third index to subset on the basis components, i.e. on both the columns and rows of the basis matrix and mixture coefficient respectively. It can be a numeric, logical, or character vector (whose elements must match the basis names of x). In the case of a logical vector the entries are recycled if necessary. Note that only the first extra subset index is used. A warning is thrown if more than one extra argument is passed in ....
drop
single logical value used to drop the NMF-class wrapping and only return subsets of one of the factor matrices:
  • When drop=FALSE it returns the NMF object x with the basis matrix and/or mixture coefficient matrix subset accordingly to the values in i, j, and ....
  • When drop=TRUE it returns the factor that is subset "the more" (see section Value).
Note that in the case where both indexes i and j are provided, argument drop is ignored: x[i,j, drop=TRUE] (resp. x[i,j,k, drop=TRUE]) is identical to x[i,j, drop=FALSE] (resp. x[i,j,k, drop=FALSE]).
x
object from which to extract element(s) or in which to replace element(s).

Details

It allows to consistently subset one or both matrix factors in the NMF model, as well as retrieving part of the basis components or part of the mixture coefficients with a reduced amount of code.

The returned value depends on the number of subset index passed and the value of argument drop:

  • No index as in x[] or x[,]: the value is the object x unchanged.

  • One single index as in x[i]: the value is the complete NMF model composed of the selected basis components, subset by i. If argument drop is not missing then only the basis matrix is returned and drop is used: x[i, drop=TRUE.or.FALSE] <=> basis(x)[, i, drop=TRUE.or.FALSE].

    Note that in version <= 0.8.7, the call x[i] was equivalent to basis(x)[, i, drop=TRUE.or.FALSE].

  • More than one index with drop=FALSE (default) as in x[i,j], x[i,], x[,j], x[i,j,k], x[i,,k], etc...: the value is a NMF object whose basis and/or mixture coefficient matrices have been subset accordingly. The third index k affects simultaneously the columns of the basis matrix AND the rows of the mixture coefficient matrix.

  • More than one index with drop=TRUE and i xor j missing: the value returned is the matrix that is the more affected by the subset index. That is that x[i, , drop=TRUE] and x[i, , k, drop=TRUE] return the basis matrix subset by [i,] and [i,k] respectively, while x[, j, drop=TRUE] and x[, j, k, drop=TRUE] return the mixture coefficient matrix subset by [,j] and [k,j] respectively.