dayoff is a teaching-focused package based largely off of material adapated from Dr. Avril Coghlan’s A little book of R for bioinformatics.
The package is named in honor of pioneering biochemist and bioinformatician Margaret Dayoff and features lessons (written by Nathan Brouwer) exploring the class PAM matrcies used for scoring protein alignment
dayoff can be installed from GitHub using the devtools package.
If you do not have the devtools installed run install.packages(“devtools”) first to download it. (I have commented this out in case you already have devtools. devtools is a package which is used by R package developers it has special functionality for downloading packages that have not been released on the offical CRAN website.
With devtools, run devtools::install_github(“brouwern/dayoff”) to download dayoff. (The install_github() comamnd lets you download a package which is in a GitHub code repository (“repo”)).
Remember to load the package into your R session using library
A dataset included in dayoff is from Higgs 2009 and contains information about the chemical properties of amino acids.
Make a histogram of from the data; You’ll git some red text in the console; no worries
dayoff off relies on a number of dependencies. If you get an error after running library(dayoff) it may be due to an issue installing one of these packages, which you might be able to resolve by downloading the package by hand. A list of dependecies is below. They can be installed using the install.packages command, which was shown above for downloading devtools