[R] How to more efficently read in a big matrix

affy snp affysnp at gmail.com
Sat Nov 10 05:52:44 CET 2007

Hi Jim,

Thanks a lot! I am currently running it on my laptop but without any
success. I could upload it to a server which is with 8Gb memory
and it might be better to go from there.

Actually, I could have the whole file splitted in two parts,
one with 2nd column to 95th column, the other one with
the rest of columns. However, I need all rows for the
two parts.

The file is in txt format and around 480Mb, very large though.
Yes, it is of numeric values.

I appreciate!


On Nov 9, 2007 11:46 PM, jim holtman <jholtman at gmail.com> wrote:
> If they are all numeric, you can use 'scan' to read them in.  With
> that amount of data, you will need almost 1GB to contain the single
> object.  If you want to do any processing, you will probably need a
> machine with at least 3-4GB of physical memory, preferrably a 64-bit
> version of R.  What type of computer are you using?  Do you really
> need all the data in at once, or can you process it in smaller batches
> (e.g., 20,000 rows at a time)?  So a little more detail on what you
> actually want to do with the data would be useful, since it does
> create a very large object.  BTW how large is the file you are reading
> and what is its format?  Have you considered a database with this
> amount of data?
> On Nov 9, 2007 11:39 PM, affy snp <affysnp at gmail.com> wrote:
> > Dear list,
> >
> > I need to read in a big table with 487 columns and 238,305 rows (row names
> > and column names are supplied). Is there a code to read in the table in
> > a fast way? I tried the read.table() but it seems that it takes forever :(
> >
> > Thanks a lot!
> >
> > Best,
> >    Allen
> >
> > ______________________________________________
> > R-help at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
> --
> Jim Holtman
> Cincinnati, OH
> +1 513 646 9390
> What is the problem you are trying to solve?

More information about the R-help mailing list