# Transforming from Mixed-sign to Nonnegative Data `nneg` is a generic function to transform a data objects that contains negative values into a similar object that only contains values that are nonnegative or greater than a given threshold. `posneg` is a shortcut for `nneg(..., method='posneg')`, to split mixed-sign data into its positive and negative part. See description for method `"posneg"`, in `nneg`. `rposneg` performs the "reverse" transformation of the `posneg` function. methods ```r nneg(object, ...) ## S4 method for signature 'matrix' nneg(object, method = c("pmax", "posneg", "absolute", "min"), threshold = 0, shift = TRUE) posneg(...) rposneg(object, ...) ## S4 method for signature 'matrix' rposneg(object, unstack = TRUE) ``` ## Arguments - `object`: The data object to transform - `...`: extra arguments to allow extension or passed down to `nneg,matrix` or `rposneg,matrix` in subsequent calls. - `method`: Name of the transformation method to use, that is partially matched against the following possible methods: - **pmax**: Each entry is constrained to be above threshold `threshold`. - **posneg**: The matrix is split into its "positive" and "negative" parts, with the entries of each part constrained to be above threshold `threshold`. The result consists in these two parts stacked in rows (i.e. `rbind`-ed) into a single matrix, which has double the number of rows of the input matrix `object`. - **absolute**: The absolute value of each entry is constrained to be above threshold `threshold`. - **min**: Global shift by adding the minimum entry to each entry, only if it is negative, and then apply threshold. - `threshold`: Nonnegative lower threshold value (single numeric). See argument `shit` for details on how the threshold is used and affects the result. - `shift`: a logical indicating whether the entries below the threshold value `threshold` should be forced (shifted) to 0 (default) or to the threshold value itself. In other words, if `shift=TRUE` (default) all entries in the result matrix are either 0 or strictly greater than `threshold`. They are all greater or equal than `threshold` otherwise. - `unstack`: Logical indicating whether the positive and negative parts should be unstacked and combined into a matrix as `pos - neg`, which contains half the number of rows of `object` (default), or left stacked as `[pos; -neg]`. ## Returns an object of the same class as argument `object`. an object of the same type of `object` ## Methods - **nneg**: `signature(object = "matrix")`: Transforms a mixed-sign matrix into a nonnegative matrix, optionally apply a lower threshold. This is the workhorse method, that is eventually called by all other methods defined in the `NMF` package. - **nneg**: `signature(object = "NMF")`: Apply `nneg` to the basis matrix of an `NMF` object (i.e. `basis(object)`). All extra arguments in `...` are passed to the method `nneg,matrix`. - **rposneg**: `signature(object = "NMF")`: Apply `rposneg` to the basis matrix of an `NMF` object. ## Examples ```r #---------- # nneg,matrix-method #---------- # random mixed sign data (normal distribution) set.seed(1) x <- rmatrix(5,5, rnorm, mean=0, sd=5) x # pmax (default) nneg(x) # using a threshold nneg(x, threshold=2) # without shifting the entries lower than threshold nneg(x, threshold=2, shift=FALSE) # posneg: split positive and negative part nneg(x, method='posneg') nneg(x, method='pos', threshold=2) # absolute nneg(x, method='absolute') nneg(x, method='abs', threshold=2) # min nneg(x, method='min') nneg(x, method='min', threshold=2) #---------- # nneg,NMF-method #---------- # random M <- nmfModel(x, rmatrix(ncol(x), 3)) nnM <- nneg(M) basis(nnM) # mixture coefficients are not affected identical( coef(M), coef(nnM) ) #---------- # posneg #---------- # shortcut for the "posneg" transformation posneg(x) posneg(x, 2) #---------- # rposneg,matrix-method #---------- # random mixed sign data (normal distribution) set.seed(1) x <- rmatrix(5,5, rnorm, mean=0, sd=5) x # posneg-transform: split positive and negative part y <- posneg(x) dim(y) # posneg-reverse z <- rposneg(y) identical(x, z) rposneg(y, unstack=FALSE) # But posneg-transformation with a non zero threshold is not reversible y1 <- posneg(x, 1) identical(rposneg(y1), x) #---------- # rposneg,NMF-method #---------- # random mixed signed NMF model M <- nmfModel(rmatrix(10, 3, rnorm), rmatrix(3, 4)) # split positive and negative part nnM <- posneg(M) M2 <- rposneg(nnM) identical(M, M2) ``` ## See Also `pmax` Other transforms: `t.NMF`

nneg function