[R] efficiently replacing values in a matrix

[Rolf Turner]

On 17/04/2008, at 7:52 AM, Matthew Keller wrote:

> Hello all,
>
> I should probably know this by now... Anyway:
>
> I have a large matrix (dim(data) is 3000  18000). In each element are
> one of the following character strings "0/0", "1/1", "1/2", "2/2". I
> wanted to replace "0/0" with NA and the other three with 0,1,2
> respectively. To accomplish just the first of these four steps I did
> this:
>
> data[data=="0/0"] <- NA
>
> Which is still running after 13 hours. I have 18 GB RAM and running 64
> bit R. What is a more efficient way to accomplish this (I've already
> done it using sed in UNIX - but want to know how to do so in R)?
> Thanks in advance.

Well I just did

	gorp <- c("0/0","1/1","1/2","2/2")
	mung <- matrix(sample(gorp,54e6,TRUE),3000,18000)
	mung[mung=="0/0"] <- NA

and the whole schmear ran in under half a minute of real time.

 > sessionInfo()
R version 2.6.2 (2008-02-08)
i386-apple-darwin8.10.1

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] misc_0.0-2

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17

I would say that something is seriously snarled up in your system.

	cheers,

		Rolf Turner

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