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...]

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...]
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