sleq

A sleek package to deal with sequences in R. Joint O'Meara lab project.

This will be developed at an inhouse hackathon on Oct. 12, 2015. A secondary objective is to make useful code, but the primary objectives are learning and lab bonding. To that end:

• We will be using roxygen2 for documentation
• We are doing unit testing with testthat -- intro here. In our case, we will write tests for a function, which it will fail at first, then we will write code to make it work.
• We will be doing pair programming: this results in better code, but more importantly helps the primary objectives of learning and bonding (unless the pairs fight, in which case it becomes learning that you're not bonding).
• We'll be using Google's R style guide.
• We may try using Gitter for communication during the hackathon (though we'll all be in the same room, it can be less distracting than shouting "Hey, you!"). Connect here. Note that it is public: this makes it easier to join, but make sure you don't say anything you don't want everyone to see.
• We are using a shared github repo (here!). Note that if you submit new code by doing pull requests, you can get a free, geeky t-shirt
• Lab members: before we start, get a github account. I advise using a permanent email address (UT will kick you out after you leave).

Some notable features of the sleq package:

• Sequences are stored as character matrices, thus easy to subset.
• However, we also have a seqalignment class. It can be indexed using [] as with a character matrix, but actually stores this internally. The object also has info about gene locations and sequence type.