[This article was first published on Recipes, scripts and genomics, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here)
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.
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/< wbr>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.
R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you're looking to post or find an R/data-science job.
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.