# nonzero: Methods for Function nonzero In Ringo: R Investigation of ChIP-chip Oligoarrays

## Description

Auxiliary functions to retrieve the indices of non-zero elements in sparse matrices.

## Value

A two-column matrix. Each row gives the row and column index of a non-zero element in the supplied matrix `x`.

## Methods

x = "dgCMatrix"

returns the indices of non-zero elements in matrices of class `dgCMatrix`

x = "matrix.csr"

returns the indices of non-zero elements in matrices of class `matrix.csr`

x = "matrix"

returns the indices of non-zero elements in matrices of base class `matrix`; equivalent to `which(x != 0, arr.ind=TRUE)`

## Note

Originally we used the `matrix.csr` class from SparseM, but we have switched to the class `dgCMatrix` from package Matrix, as that package is part of the R distribution bundle now.

The idea is to have a function similar to `which(x != 0, arr.ind=TRUE)` if `x` is a matrix.

`dgCMatrix-class`
 ```1 2 3 4 5 6 7``` ``` (A <- matrix(c(0,0,0,0,0,1,0,0,0,0,0,0,0,0,-34), nrow=5, byrow=TRUE)) str(A.dgc <- as(A, "dgCMatrix")) nonzero(A.dgc) A2.dgc <- Matrix::cBind(A.dgc, A.dgc) as.matrix(A2.dgc) nonzero(A2.dgc) ```