Articles by altuna

Calling BEDtools from R

February 22, 2011 | altuna

BEDtools suite provides command-line functionality when dealing with genomic coordinate based operations, such as overlapping bed files or getting coverage of a bed file over a genome (similar, not exactly same, functionality in R is provided by IRange... [Read more...]

Utilizing multiple cores in R

February 8, 2011 | altuna

There are a couple of options in R, if you want to utilize multiple cores on your machine. These days my favorite is doMC package, which depends on foreach and multicore packages.in the section below squareroot for each number is calculated in parallel... [Read more...]

command line options in R: "optparse" package

February 8, 2011 | altuna

C/python style option parsing now available in R with "optparse" package. Check the documentation here and see below to see how it worksuser@node002 scripts $ Rscript filter.transcripts.by.ncRNA.R -husage:  usage: filter.transcripts.by.ncRNA.R [op... [Read more...]

sqldf and grouping rows in R

February 8, 2011 | altuna

In R, you can treat tables (or data.frames as they are called in R) as SQL tables. That means you can query them as you would query a database with SQL commands. This is particularly useful 1) if you know SQL, hahah:)  2) if you have large tabl... [Read more...]
1 2

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)