Re: [Rd] Compression of largish expression array files in the DAAGbio/inst/doc directory?
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.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@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, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compression of largish expression array files in the DAAGbio/inst/doc directory?
Thanks. That seems to work. John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +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 On 09/04/2011, at 4:58 PM, Prof Brian Ripley wrote: 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.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@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, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Compression of largish expression array files in the DAAGbio/inst/doc directory?
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.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
