Write a Sparse Matrix to a CSV in R

Question

I have a sparse matrix (dgCMatrix) as the result of fitting a glmnet. I want to write this result to a .csv but can't use write.table() the matrix because it can't coerced into a data.frame.

Is there a way to coerce the sparse matrix to either a data.frame or a regular matrix? Or is there a way to write it to a file while keeping the coefficient names which are probably row names?

Answer 1

That will be dangerous to transform the sparse matrix to a normal one, if the sparse matrix size is too large. In my case (text classification task), I got a matrix of size 22490 by 120,000. If you try get the dense matrix, that will be more than 20 GB, I think. Then R will break down !

So my suggestion, you may simply store the sparse matrix in an efficient and memory friendly way, such as Matrix Market Format, which keeps all non-zero values and their coordinates (row & col number). In the R you can use the method writeMM

Answer 2

as.matrix() will convert to the full dense representation:

> as.matrix(Matrix(0, 3, 2))
     [,1] [,2]
[1,]    0    0
[2,]    0    0
[3,]    0    0

You can write the resulting object out using write.csv or write.table.