Joschi - 1 year ago 56

R Question

I just wrote a very basic function for the z tranformation in a Matrix over all columns. It looks like this:

`sapply(MyObject, function(x){(x-mean(x))/sd(x)})`

I randomly checked my function for some cells within the Matrix and it seems to work fine. Still I wanted to confirm the function is okay, because I'm very new to R and I could not find any good examples on the internet.

Answer Source

You should look at `scale()`

which does this for you.

Your function is close to being correct; you should add `na.rm = TRUE`

to both the `sd()`

and `mean()`

function calls.

I would write (if not using `scale()`

) the function using `sweep()`

instead of the `sapply()`

. E.g.

```
ztran <- function(x, na.rm = TRUE) {
mns <- colMeans(x, na.rm = na.rm)
sds <- apply(x, 2, sd, na.rm = na.rm)
x <- sweep(x, 2, mns, "-")
x <- sweep(x, 2, sds, "/")
x
}
```

In use we have

```
> df <- data.frame(matrix(1:9, ncol = 3))
> ztran(df)
X1 X2 X3
1 -1 -1 -1
2 0 0 0
3 1 1 1
> scale(df)
X1 X2 X3
[1,] -1 -1 -1
[2,] 0 0 0
[3,] 1 1 1
attr(,"scaled:center")
X1 X2 X3
2 5 8
attr(,"scaled:scale")
X1 X2 X3
1 1 1
```

`sweep`

is a very useful vectorised tool for this sort of operation. Notice also that `sapply()`

simplifies to a matrix, which may not be what you wanted. `sweep()`

doesn't do this:

```
> class(ztran(df))
[1] "data.frame"
> class(sapply(df, function(x){(x-mean(x))/sd(x)}))
[1] "matrix"
```