q2e

q2e is an R package that uses a genetic algorithm to determine the extent of deamidation that gives the best fit to a measured distribution of masses for glutamine.

Installing

You'll need the devtools package to install q2e so either do this:

> require("devtools")

or this:

> install.packages("devtools")

> library(devtools)

Then you can use the install_github function to install q2e. As this package is in development, it's best to use the force option. Also, the documentation for the package is saved in vignettes, so you probably want to set build_vignettes=T so that these are installed:

> devtools::install_github("https://github.com/bioarch-sjh/q2e",subdir = "q2e",force=T,build_vignettes=T)

Of course, you'll only need to do that once for your R installation. After that, whenever you want to use q2e, simply enter:

> library("q2e")

Documentation

The documentation (still in development) for q2e is available in vignettes for the package. To see these guides, enter:

> browseVignettes("q2e")

This will open a page in your browser that will list the available documentation

C Code

For reference, Julie Wilson's original C code is in the directory 'jwc'. A modified version of this code is in the q2e 'src' subdirectory, but the modifocations simply allow the Rcpp compiler to access the functions.

Academic Referencing

This software is free, but if you use it in an academic paper, please cite the following:

Julie Wilson, Nienke L. van Doorn and Matthew J. Collins (2012). Assessing the extent of bone degradation using glutamine deamidation in collagen. Anal. Chem. 84(21), 9041-9048.

folders

• crinkle contains the original isodists C code developed by Julie Wilson
• raw contains the original q2e C code developed by Julie Wilson