command line options in R: "optparse" package

February 8, 2011

(This article was first published on Recipes, scripts and genomics, and kindly contributed to R-bloggers)

C/python style option parsing now available in R with “optparse” package. Check the documentation here and see below to see how it works

[email protected] scripts $ Rscript -h
usage:  usage: [options]

    -i INPUTFILE, –inputfile=INPUTFILE
        a BED12 file with transcripts [default /home/user/tx.db.bed]

    -o OUTPUTPATH, –outputpath=OUTPUTPATH
        /output/path/string to be used for output files [default “/home/user/projects/

    -a ANNOTATION, –annotation=ANNOTATION
        annotation BED12 file containing  ncRNA locations [default /home/user/projects/annotations/frna.db.hg18.bed]

    -h, –help
        Show this help message and exit

To leave a comment for the author, please follow the link and comment on their blog: Recipes, scripts and genomics. offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...

If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Comments are closed.

Search R-bloggers


Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)