Alternative to Super-Assignment: <<-

See Permanent and temporary Objects with R

set.seed(1)  # make it reproducible

Creating matrix inside a function:

mat <- function() {

    matrix0 <- matrix(rexp(25, rate = 0.1), ncol = 5)
    matrix0[1, 1] <- NA
    matrix1 <<- na.omit(matrix0)

}

List objects:

ls()

## [1] "mat"

matrix0 doesn't exist outside the function environment, unless created outside that function. Nor does matrix1, despite super-assignment.

Once defined in the global environment it does exist:

matrix0 <- matrix(rexp(25, rate = 0.1), ncol = 5)
matrix0

##        [,1]   [,2]  [,3]   [,4]   [,5]
## [1,]  7.552 28.950 13.91 10.352 23.645
## [2,] 11.816 12.296  7.62 18.760  6.419
## [3,]  1.457  5.397 12.38  6.547  2.941
## [4,]  1.398  9.566 44.24  3.369  5.659
## [5,]  4.361  1.470 10.55  5.885  1.061

ls()

## [1] "mat"     "matrix0"

matrix1 won't exist unless captured as output from the function:

mat <- function(x) {
    x[1, 1] <- NA
    na.omit(x)
}

matrix1 <- mat(matrix0)
matrix1

##        [,1]   [,2]  [,3]   [,4]  [,5]
## [1,] 11.816 12.296  7.62 18.760 6.419
## [2,]  1.457  5.397 12.38  6.547 2.941
## [3,]  1.398  9.566 44.24  3.369 5.659
## [4,]  4.361  1.470 10.55  5.885 1.061
## attr(,"na.action")
## [1] 1
## attr(,"class")
## [1] "omit"

identical(matrix0, matrix1)  # true/false

## [1] FALSE

all.equal(matrix0, matrix1)  # comparison

## [1] "Attributes: < Length mismatch: comparison on first 1 components >"
## [2] "Attributes: < Component \"dim\": Mean relative difference: 0.2 >" 
## [3] "Numeric: lengths (25, 20) differ"

Or creating matrix0 inside the function:

remove(matrix0)  # remove existing object

mat2 <- function(n, rate = 1, ncol) {
    set.seed(1)
    x <- matrix(rexp(n, rate), ncol)
    x[1, 1] <- NA
    na.omit(x)
}

matrix1 <- mat2(n = 25, rate = 0.1, ncol = 5)

matrix1

##        [,1]   [,2]  [,3]   [,4]  [,5]
## [1,] 11.816 12.296  7.62 18.760 6.419
## [2,]  1.457  5.397 12.38  6.547 2.941
## [3,]  1.398  9.566 44.24  3.369 5.659
## [4,]  4.361  1.470 10.55  5.885 1.061
## attr(,"na.action")
## [1] 1
## attr(,"class")
## [1] "omit"

ls()

## [1] "mat"     "mat2"    "matrix1"