From ripley at stats.ox.ac.uk  Sat Apr  9 08:58:41 2011
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Sat, 9 Apr 2011 07:58:41 +0100 (BST)
Subject: [Rd] Compression of largish expression array files in the
 DAAGbio/inst/doc directory?
In-Reply-To: <51284363-243E-40B3-933A-B28F05986CBD@anu.edu.au>
References: <51284363-243E-40B3-933A-B28F05986CBD@anu.edu.au>
Message-ID: <alpine.LFD.2.02.1104090748410.21478@gannet.stats.ox.ac.uk>

As far as I can see read.maimages is built on top of R's own 
file-reading facilties, and they all read compressed (but not zipped) 
files as from R 2.10.0.

So simply use

gzip -9 coral55?.spot

and rename the files back to *.spot.

If you need more compression, use xz -9e.  (You can also do this in R: 
readLines() on the file, writeLines() using gzfile or xzfile.)

You will need to make the package 'Depends: R (>= 2.10)'.

On Sat, 9 Apr 2011, John Maindonald wrote:

> The inst/doc directory of the DAAG package has 6 files coral551.spot, ... that
> are around 0.85 MB each.  It would be useful to be able to zip then, but that
> as matters stand interferes with the use of the Sweave file that uses them to
> demonstrate input of expression array data that is in the "spot" format.  They
> do not automatically get unzipped when required.  I have checked that
> read.maimages (in limma) does not, unless I have missed something, have
> an option for reading zipped files.  Is there any way to get around this without
> substantially complicating the exposition in marray-notes.pdf (also in the
> inst/doc subdirectory)?
>
> John Maindonald             email: john.maindonald at anu.edu.au
> phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
> Centre for Mathematics & Its Applications, Room 1194,
> John Dedman Mathematical Sciences Building (Building 27)
> Australian National University, Canberra ACT 0200.
> http://www.maths.anu.edu.au/~johnm
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] Compression of largish expression array files in the DAAGbio/inst/doc directory?
Prof Brian Ripley