Importing, subsetting, merging and exporting various text files with annotation (in the wide sense, i.e. anything that might help when interpreting your experiment) is not computation and it’s not biology either, but it’s housekeeping that needs to be done. Everyone has a weapon of choice for general-purpose ... [Read more...]

I think you’ve noticed by now that a normal interactive R session is quite messy. If you don’t believe me, try playing around for a while and then give the history() command, which will show you the commands you’ve typed. If you’re anything like me, a ... [Read more...]

Let’s look at my gff track headers again. Why not do it with plyr instead? d_ply splits the data frame by the feature column and applies a nameless function that writes subsets to the file (and returns nothing, hence the ”_” in the name). This isn’t shorter or ... [Read more...]

The other day, I wanted to add track lines to a GFF file, so that I could view different features as separate custom tracks in a genome browser. The need to shuffle genome coordinates between different file formats seems to occur all the time when you deal with some kind ... [Read more...]

In part I, we looked at importing data into R and simple ways to manipulate data frames. Once we’ve gotten our data safely into R, the first thing we want to do is probably to make some plots. Below, we’ll make some simple plots of the made-up comb ... [Read more...]

Note in Swedish: Jag hoppas läsaren ursäktar att jag skriver på engelska då och då. This will be a brief introduction to using the statistics software R for biologists who want to do some of their data analysis in R. There are plenty of introductions to R (see ... [Read more...]