https://github.com/tnaake/msqualityutils

https://github.com/tnaake/msqualityutils

mass-spectrometry metabolomics proteomics qc r

Last synced: 3 months ago
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• Host: GitHub
• URL: https://github.com/tnaake/msqualityutils
• Owner: tnaake
• Created: 2021-12-20T16:44:34.000Z (over 3 years ago)
• Default Branch: devel
• Last Pushed: 2023-03-14T15:22:42.000Z (about 2 years ago)
• Last Synced: 2023-12-13T03:50:31.357Z (over 1 year ago)
• Topics: mass-spectrometry, metabolomics, proteomics, qc, r
• Language: R
• Homepage:
• Size: 1.63 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# MsQualityUtils

[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)

![R-CMD-check-bioc](https://github.com/tnaake/MsQualityUtils/workflows/R-CMD-check-bioc/badge.svg)

[![codecov.io](http://codecov.io/github/tnaake/MsQualityUtils/coverage.svg?branch=master)](http://codecov.io/github/tnaake/MsQualityUtls?branch=main)

[![license](http://img.shields.io/badge/license-GPL%20%28%3E=%203%29-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-3.0.html)

Creation of MsExperiment objects for MsQuality-based QC metric calculation

## Description

Data quality assessment is an integral part of preparatory data analysis 

to ensure sound biological information retrieval. 

We present here the `MsQualityUtils` package, which provides functionality to create

`MsExperiment` objects from mzML and MetIDQ-derived files. 

The `MsExperiment` files can subsequently be used to calculate quality metrics 

at the per-sample level using the 

[`MsQuality`](https://github.com/tnaake/MsQuality) package. 

`MsQuality` relies on the [`mzQC`](https://github.com/HUPO-PSI/mzQC) 

framework of quality metrics defined by the Human Proteome 

Organization-Proteomics Standards Intitiative (HUPO-PSI). 

The `MsQuality` package is built upon the `Spectra` and the `MsExperiment` package.

Metrics will be calculated based on the information stored in a 

`Spectra` object, thus, the spectral data of each sample should be stored

in one `Spectra` object. The `MsExperiment` serves as a container to 

store the mass spectral data of multiple samples. `MsQuality` enables the user

to calculate quality metrics both on `Spectra` and `MsExperiment` objects. 

The `MsQualityUtils` package provides functionality to create `MsExperiment` 

objects that store the (spectral) information of mzML or MetIDQ files. 

## Contact 

You are welcome to 

 * write a mail to  

 * submit suggestions and issues: 

 * send a pull request:  

## Install

To install `MsQualityUtils`, you have first to install the 

[devtools](http://cran.r-project.org/web/packages/devtools/index.html) package: 

```r

install.packages("devtools")

library("devtools")

```

Install the `MsQualityUtils` package then via

```r

install_github("tnaake/MsQualityUtils")

```