Creation, Reading and Validation of 'mzqc' Files

Reads, writes and validates 'mzQC' files. The 'mzQC' format is a standardized file format for the exchange, transmission, and archiving of quality metrics derived from biological mass spectrometry data, as defined by the HUPO-PSI (Human Proteome Organisation - Proteomics Standards Initiative) Quality Control working group. See < https://hupo-psi.github.io/mzQC/> for details.

rmzqc

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.

## CRAN
install.packages("rmzqc")

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:

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

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:

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

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).

Building the package locally

Use roxygen2 to build the vignettes and documentation:

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

Use pkgdown to build the html documentation in ./docs/:

pkgdown::buildsite()

Links

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