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

[affy snp]

Hi Gabor,

Thanks a lot!

The header of the big file looks like as follows:

probe_set
WM_806_Signal_A
WM_806_call
WM_1716_Signal_A
WM_1716_call
....

I only need those columns with the header as like _Signal_A

Can you suggest how to use sqldf?

Thanks!

Allen

On Nov 9, 2007 11:47 PM, Gabor Grothendieck <ggrothendieck at gmail.com> wrote:
> 1. You might be able to speed it up somewhat by specifying
> colClasses=.
>
> 2. Another possibility is that the devel version of
> the sqldf package provides an interface which simplifies reading a data file
> into sqlite and from there into R.  This is particularly useful if you
> don't want to read it all in.  See example 6 on the home page:
> http://sqldf.googlecode.com
>
> 3. If it doesn't change and its ok to read it in slowly once then just
> read it in slowly and save() it.  Then you can load()
> it on subsequent runs which should be fast.
>
> 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.
> >
>