Yoo should have a look at ?write.table dataset <- cbind(foo, bar, qux) #write to a file write.table(x = dataset, file = "your_file_name.txt", sep = "\t", row.names = FALSE) #wrfite to the console write.table(x = dataset, file = "", sep = "\t", row.names = FALSE)
HTH, Thierry ------------------------------------------------------------------------ ---- ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -----Oorspronkelijk bericht----- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Gundala Viswanath Verzonden: donderdag 8 januari 2009 14:27 Aan: jim holtman CC: r-h...@stat.math.ethz.ch Onderwerp: Re: [R] Faster Printing Alternatives to 'cat' Dear Jim and Henrik, > What exactly is the problem you are trying to solve. > Is it going to be read by some other program? I simply want to print the data out. Surely, this data will be manipulated (with Excel or other programming languages) by other people suit to their purpose. Typically the print out from the loop looks like this: ATCGATCGATCGGGGGGGGGGGGGGGTTTGCGGG 10 11.992 CCCCCCCCGGGCCATCGGTCAGGGAATTGACGGAA 2 0.222 ..... up to ~16 million lines. > How much physical memory do you have on your machine? 6GB > Is there paging occuring due to the size of the objects? Don't quite understand what do you mean by that So sorry for my lack of knowledge in R. > Have you consider creating a structure with 10,000 of the variables > each time through the loop and then writing them out? Never thought about that. Can you be specific how can this be achieved? - Gundala Viswanath Jakarta - Indonesia On Thu, Jan 8, 2009 at 10:10 PM, jim holtman <jholt...@gmail.com> wrote: > What exactly is the problem you are trying to solve. What is going to > be done with the data? Is it going to be read by some other program? > How much physical memory do you have on your machine? Is there paging > occuring due to the size of the objects? Have you consider creating a > structure with 10,000 of the variables each time through the loop and > then writing them out? A lot will depend on how much free memory you > have. I will also ask one of my favorite questions; "tell me what you > want to do, not how you want to do it". > > On Thu, Jan 8, 2009 at 6:12 AM, Gundala Viswanath <gunda...@gmail.com> wrote: >> Dear all, >> >> I found that printing with 'cat' is very slow. >> >> For example in my machine this snippet >> >> __BEGIN__ >> >> # I need to resolve to use this type of loop. >> # because using write(), I need to create a matrix which >> # consumes so much memory. Note that "foo, bar, qux" object >> # is already very large (>2Gb) >> >> for ( s in 1:length(x) ) { >> cat(as.character(foo[s]),"\t",bar[s],"\t", qux[s],"\n") >> } >> __END__ >> >> for "x" of size ~1.5million, takes more than 10 hours to print. >> On my Linux 1994.MHz AMD processor. >> >> Is there any faster alternatives to "cat" ? >> >> >> - Gundala Viswanath >> Jakarta - Indonesia >> >> ______________________________________________ >> R-help@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 that you are trying to solve? > ______________________________________________ R-help@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. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. ______________________________________________ R-help@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.
