command line options in R: "optparse" package

February 8, 2011
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(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 filter.transcripts.by.ncRNA.R -h
usage:  usage: filter.transcripts.by.ncRNA.R [options]

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/
transcripts”]

    -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

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