On Mon, 23 Mar 2009, David Reiss wrote:
I have a very large tab-delimited file, too big to store in memory via
readLines() or read.delim(). Turns out I only need a few hundred of those
lines to be read in. If it were not so large, I could read the entire file
in and "grep" the lines I need. For such a large file; many calls to
read.delim() with incrementing "skip" and "nrows" parameters, followed by
grep() calls is very slow.
You certainly don't want to use repeated reads from the start of the file with
skip=, but if you set up a file connection
fileconnection <- file("my.tsv", open="r")
you can read from it incrementally with readLines() or read.delim() without
going back to the start each time.
The speed of approach should be within a reasonable constant factor of anything
else, since reading the file once is unavoidable and should be the bottleneck.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.edu University of Washington, Seattle
______________________________________________
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.
