From: Ramon Diaz-Uriarte <rdiaz02_at_gmail.com>

Date: Fri, 29 Feb 2008 19:04:01 +0100

Date: Fri, 29 Feb 2008 19:04:01 +0100

Thanks, Greg. Yes, I'd store the compressed stuff as a raw data type.

Best,

R.

On Thu, Feb 28, 2008 at 11:54 PM, Gregory Warnes <gregory.warnes_at_mac.com> wrote:

*>
*

> You might look at storing the data using R's "raw" data type...

*>
**> -G
**>
**>
**>
**>
**> On Feb 28, 2008, at 5:38PM , Ramon Diaz-Uriarte wrote:
**>
**> > Dear Christos,
**> >
**> > Thanks for your reply. Actually, I should have been more careful with
**> > language: its not really a sparse matrix, but rather a ragged array
**> > that results from a more compact representation we though of for the
**> > hidden states in a Hidden Markov Model in many runs of MCMC. However,
**> > it might make sense for us to check sparseMatrix and see how its done
**> > there.
**> >
**> > Thanks,
**> >
**> > R
**> >
**> > On Thu, Feb 28, 2008 at 7:49 PM, Christos Hatzis
**> > <christos.hatzis_at_nuverabio.com> wrote:
**> >> Ramon,
**> >>
**> >> If you are looking for a solution to your specific application
**> >> (as opposed
**> >> to a general compression/ decompression mechanism), it might be
**> >> worth
**> >> checking out the Matrix package, which has facilities for storing
**> >> and
**> >> manipulating sparse matrices. The sparseMatrix class stores
**> >> matrices in the
**> >> triplet representation (i.e. only indices and values of the non-zero
**> >> elements) and this affords great compression ratios, depending on
**> >> the size
**> >> and degree of sparseness of the matrix.
**> >>
**> >> -Christos
**> >>
**> >>
**> >>
**> >>> -----Original Message-----
**> >>> From: r-help-bounces_at_r-project.org
**> >>> [mailto:r-help-bounces_at_r-project.org] On Behalf Of Ramon Diaz-
**> >>> Uriarte
**> >>> Sent: Thursday, February 28, 2008 1:18 PM
**> >>> To: r-help_at_stat.math.ethz.ch
**> >>> Subject: [R] compress data on read, decompress on write
**> >>>
**> >>> Dear All,
**> >>>
**> >>> I'd like to be able to have R store (in a list component) a
**> >>> compressed data set, and then write it out uncompressed.
**> >>> gzcon and gzfile work in exactly the opposite direction. What
**> >>> would be a good way to handle this?
**> >>>
**> >>> Details:
**> >>> ----------
**> >>>
**> >>> We have a package that uses C; part of the C output is a
**> >>> large sparse matrix. This is never manipulated directly by R,
**> >>> but always by the C code. However, we need to store that data
**> >>> somewhere (inside an R
**> >>> object) for further calls to the functions in our package.
**> >>> We'd like to store that matrix as part of the R object (say,
**> >>> as an element of a list). Ideally, it would be stored in as
**> >>> compressed a way as possible.
**> >>> Then, when we need to use that information, it would be
**> >>> decompressed and passed to the C function.
**> >>>
**> >>> I guess one way to do it is to have C deal with the
**> >>> compression and uncompression (e.g., using zlib or the bzip2
**> >>> libraries) and then use readBin, etc, from R. But, if I can,
**> >>> I'd like to avoid our C code having to call zlib, etc, so as
**> >>> to make our package easily portable.
**> >>>
**> >>>
**> >>> Thanks,
**> >>>
**> >>> R.
**> >>>
**> >>> --
**> >>> Ramon Diaz-Uriarte
**> >>> Statistical Computing Team
**> >>> Structural Biology and Biocomputing Programme Spanish
**> >>> National Cancer Centre (CNIO) http://ligarto.org/rdiaz
**> >>>
**> >>> ______________________________________________
**> >>> 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.
**> >>>
**> >>>
**> >>
**> >>
**> >>
**> >
**> >
**> >
**> > --
**> > Ramon Diaz-Uriarte
**> > Statistical Computing Team
**> > Structural Biology and Biocomputing Programme
**> > Spanish National Cancer Centre (CNIO)
**> > http://ligarto.org/rdiaz
**> >
**> > ______________________________________________
**> > 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.
**>
**>
*

-- Ramon Diaz-Uriarte Statistical Computing Team Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz ______________________________________________ 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.Received on Fri 29 Feb 2008 - 18:06:39 GMT

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