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An R package for reading, validating, and writingmzQC files.

You can grabrmzqc 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.

## CRANinstall.packages("rmzqc")

or

## GitHubif (!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:

help(package="rmzqc")browseVignettes(package = 'rmzqc')

Please feel free to report bugs (see below), or issue pull requests!

Check the version history inNEWS.md.

The package vignettes provide examples on how to usermzqc.After the package is installed (see below),you can browse the vignettes using either of these commands within R:

help(package="rmzqc")browseVignettes(package = 'rmzqc')

If you do not want to wait that long, you can look at thelatest online vignette at CRAN

Currently, there are vignettes on:

• Creating and storing a basic mzQC document usingrmzqc(more to come)

If you encounter a bug, please use theGitHub issue tracker and file a report.

You should include

• stage you encounter the bug, e.g. during installation, importing, exporting, etc
• version ofrmzqc, e.g. callhelp(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 orderto track down the issue.In certain situations, the input/output file you are trying to read/write is helpful.

We welcome input from our user base!rmzqc has a very permissiveMIT License (seeDESCRIPTION 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 openinga 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 aPull Request (PR).

Useroxygen2 to build the vignettes and documentation:

roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))

Usepkgdown to build the html documentation in ./docs/:

pkgdown::buildsite()

Seehttps://github.com/HUPO-PSI/mzQC/ for the specification details of the mzQC format.