An R package for reading, validating, and writing mzQC files.
Installation
You can grab rmzqc from either CRAN or GitHub. GitHub installation will give you the latest package; the CRAN version might be a little older, but is faster to install.
or
## GitHub
if (!require(devtools, quietly = TRUE)) install.packages("devtools")
library("devtools")
install_github("MS-Quality-hub/rmzqc", build_vignettes = TRUE, dependencies = TRUE)To get started, see the help and/or vignettes:
Please feel free to report bugs (see below), or issue pull requests!
Latest changes / ChangeLog
Check the version history in NEWS.md.
Usage
The package vignettes provide examples on how to use rmzqc. After the package is installed (see below), you can browse the vignettes using either of these commands within R:
If you do not want to wait that long, you can look at the latest online vignette at CRAN
Currently, there are vignettes on: - Creating and storing a basic mzQC document using rmzqc (more to come)
Bug reporting / Feature requests
If you encounter a bug, please use the GitHub issue tracker and file a report.
You should include - stage you encounter the bug, e.g. during installation, importing, exporting, etc - version of rmzqc, e.g. call help(package="rmzqc") within R - error message (very important!). Either copy it or provide a screen shot.
Please be as precise as possible when providing the bug report: just imagine what kind of information you would like to have in order to track down the issue. In certain situations, the input/output file you are trying to read/write is helpful.
Contributing - Get Involved!
We welcome input from our user base! rmzqc has a very permissive MIT License (see DESCRIPTION file), so feel free to fork, patch and contribute!
There are many ways to get involved, you do not need to be a developer! - suggest a new metric (and why you think it’s useful) by opening a new ticket here on GitHub. - suggest changes to functions (improvements or bugfixes), see above. - suggest improvements to our documentation - write code (in R) and submit a Pull Request (PR).
Links
See https://github.com/HUPO-PSI/mzQC/ for the specification details of the mzQC format.