In lgatto/sequences: Generic and Biological Sequences

Package: sequences
Authors: r packageDescription("sequences")[["Author"]]
Last modified: r file.info("sequences.Rmd")$mtime
Compiled: r date()

Introduction

The dummy sequences package is used to illustrate the Advanced R programming and package development. It describes classes and methods to manipulate generic and biological sequences. If you are interested in real sequence manipulation in R, have a look at Biostrings, seqinr or ape, and possibly others.

This package can be installed with

remotes::install_github("lgatto/sequences")

Using `sequences`

Let's start by loading the package and read a fasta sequence that is provided with the package.

library("sequences")
fafile <- dir(system.file(package = "sequences", dir = "extdata"),
              full.name = TRUE,
              pattern = "fasta$")
fafile
myseq <- readFasta(fafile[1])
myseq

Printing the sequence displays it's sequence numbering the lines.

print(myseq)

This creates an instance of class \Sexpr{class(myseq)} that can be transcribed with the \Rfunction{transcribe} method.

transcribe(myseq)

barplot(gccount(seq(myseq)))

Background

This package is developed as part of the Advanced R programming and package development (ARPD) course, taught by Laurent Gatto and Robert Stojnic. The course has originally been set up and run as an intense 1 day course in the Graduate School of Life Sciences of the University of Cambridge. Since March 2011, the course has been run on a regular basis in the Bioinformatics Teaching Facilty in the Department of Genetics, Cambridge.

In November 2011 and December 2012, 2 day courses were taught at the EMBL in Heidelberg, on Wolfgang Huber's invitation.

knitr::include_graphics("r-advanced-course-2011.jpg")

Acknowledgements {-}

Several people have been contributed to make this course possible. David P. Judge, initially helped us to set up the course in the Bioinformatics Teaching Facilty at the Cambridge University. Wolfgang Huber, invited us at the EMBL in Heidelberg.