On 18 June 2009 at 14:02, Jim Nemesh wrote: | Actually, I'm going to take by my comments. | | You can use Rscript with multiple -e arguments to do what I was | looking for: | | Rscript -e 'library(broadgap.hapmaptools)' -e 'processAllFiles(dir="/ | humgen/cnp04/sandbox/steve/1m/hapmap3/genotypes/ftp.hapmap.org/genotypes/2008-07_phaseIII/hapmap_format/forward | ", outRootDir="/humgen/cnp04/sandbox/data/snpTagging")'
That file structure reveals that you use a Unix-alike operating system, in which case you should look at littler (which Gabor already pointed you too). I use it all the time for scripted wrappers like your case here. E.g. and obviously untested: $ r -lbroadgap.hapmaptools,getopt \ # this loads you both libraries, silently -e'processAllFiles(dir="/humgen/.../forward", outRootDir="/humgen/.../snpTagging")' where I truncated the paths and indented a line. [ In tis case we don't even need getopt, do we ? ] As a bonus, r starts up faster than Rscript [1]. And it may save you from pressing six more keys not counting Shift. Hope this helps, Dirk [1] As it embeds R rather than calls it using exec() -- at the cost of not being portable beyond Linux and OS X. -- Three out of two people have difficulties with fractions. ______________________________________________ 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.