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

user@node002 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/

    -h, --help
        Show this help message and exit

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