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

[jim holtman]

If they are all numeric, then read it in with:

x <- scan('yourfile', what=0)  # assuming blank separators

This will create a single vector of the values.  Now this comes in in
row order if that is what your data file has, so you could just add
dimensions of

dim(x) <- c(487, 238305)

rows and columns are transposed, but if you have enough memory, you
can transpose them, or just leave the data as is, and change your
processing to reorder the rows/cols.  This should lets you read it in
in the fastest manner and then play with it.

On Nov 9, 2007 11:52 PM, affy snp <affysnp at gmail.com> wrote:
> 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!
>
> Allen
>
>
>
>
>
>
> 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?
> >
>



-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?