Re: [R] tapply for enormous (2^31 row) matrices

2012-02-26 Thread Gabor Grothendieck
On Thu, Feb 23, 2012 at 11:39 AM, Matthew Keller mckellerc...@gmail.com wrote: Thank you all very much for your help (on both the r-help and the bioconductor listserves). Benilton - I couldn't get sqldf to install on the server I'm using (error is: Error : package 'gsubfn' does not have a

Re: [R] tapply for enormous (2^31 row) matrices

2012-02-23 Thread Matthew Keller
Thank you all very much for your help (on both the r-help and the bioconductor listserves). Benilton - I couldn't get sqldf to install on the server I'm using (error is: Error : package 'gsubfn' does not have a name space). I think this was a problem for R 2.13, and I'm trying to get the admin's

Re: [R] tapply for enormous (2^31 row) matrices

2012-02-22 Thread ilai
On Tue, Feb 21, 2012 at 4:04 PM, Matthew Keller mckellerc...@gmail.com wrote: X - read.big.matrix(file.loc.X,sep= ,type=double) hap.indices - bigsplit(X,1:2) #this runs for too long to be useful on these matrices #I was then going to use foreach loop to sum across the splits identified by

[R] tapply for enormous (2^31 row) matrices

2012-02-21 Thread Matthew Keller
Hi all, SETUP: I have pairwise data on 22 chromosomes. Data matrix X for a given chromosome looks like this: 1 13 58 1.12 6 142 56 1.11 18 307 64 3.13 22 320 58 0.72 Where column 1 is person ID 1, column 2 is person ID 2, column 3 can be ignored, and column 4 is how much chromosomal sharing