command line options in R: "optparse" package
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C/python style option parsing now available in R with “optparse” package. Check the documentation here and see below to see how it worksWant to share your content on R-bloggers? click here if you have a blog, or here if you don't.
user@node002 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/
-h, –help
Show this help message and exit
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