Introduction One of the best features about R is the simple way you can use a number of different strategies to create subsets of large data tables. The basic selection mechanisms you have are that you can subset a data frame by providing: A set of column or row indices A set of boolean values…
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Why is java not found on the command line after I’ve installed it?
The Problem A common problem we have reported from users of SeqMonk is that when they try to launch the program on a Windows system they get an error message saying that java could not be found, even though they have installed this and they can show that it works fine in their browser. When…
A new way to look at duplication in FastQC v0.11
Introduction After a long gestation we’ll be releasing a new version of FastQC in the near future to address some of the common problems and confusions we’ve encountered in the current version. I’ll write more about this in future posts but wanted to start with the most common complaint, that the duplicate sequence plot was…
Generating R reports with vector images from markdown with knitr
Introduction One really nice addition to a standard R environment is the ability to create reports which combine R code, comments and embedded graphical output. The original mechanism for doing this was Sweave, but more recently a second system called knitr has emerged which seems to be more flexible, and this is what I’ve been…