If they are all numeric, then read it in with: x <- scan('yourfile', what=0) # assuming blank separators
This will create a single vector of the values. Now this comes in in row order if that is what your data file has, so you could just add dimensions of dim(x) <- c(487, 238305) rows and columns are transposed, but if you have enough memory, you can transpose them, or just leave the data as is, and change your processing to reorder the rows/cols. This should lets you read it in in the fastest manner and then play with it. On Nov 9, 2007 11:52 PM, affy snp <[EMAIL PROTECTED]> wrote: > Hi Jim, > > Thanks a lot! I am currently running it on my laptop but without any > success. I could upload it to a server which is with 8Gb memory > and it might be better to go from there. > > Actually, I could have the whole file splitted in two parts, > one with 2nd column to 95th column, the other one with > the rest of columns. However, I need all rows for the > two parts. > > The file is in txt format and around 480Mb, very large though. > Yes, it is of numeric values. > > I appreciate! > > Allen > > > > > > > On Nov 9, 2007 11:46 PM, jim holtman <[EMAIL PROTECTED]> wrote: > > If they are all numeric, you can use 'scan' to read them in. With > > that amount of data, you will need almost 1GB to contain the single > > object. If you want to do any processing, you will probably need a > > machine with at least 3-4GB of physical memory, preferrably a 64-bit > > version of R. What type of computer are you using? Do you really > > need all the data in at once, or can you process it in smaller batches > > (e.g., 20,000 rows at a time)? So a little more detail on what you > > actually want to do with the data would be useful, since it does > > create a very large object. BTW how large is the file you are reading > > and what is its format? Have you considered a database with this > > amount of data? > > > > > > On Nov 9, 2007 11:39 PM, affy snp <[EMAIL PROTECTED]> 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@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 you are trying to solve? > > > -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem 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.