MsQuality
Science Score: 26.0%
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○Scientific vocabulary similarity
Low similarity (14.4%) to scientific vocabulary
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Repository
Statistics
- Stars: 7
- Watchers: 2
- Forks: 0
- Open Issues: 3
- Releases: 0
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Metadata Files
README.md
MsQuality
Calculation of QC metrics from mass spectrometry data
Description
Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval.
We present here the MsQuality package, which provides functionality to calculate
quality metrics for mass spectrometry-derived, spectral data at the per-sample
level. MsQuality relies on the mzQC
framework of quality metrics defined by the Human Proteome
Organization-Proteomics Standards Intitiative (HUPO-PSI). These metrics
quantify the quality of spectral raw files using a controlled vocabulary.
The package is especially addressed towards users that acquire
mass spectrometry data on a large scale (e.g. data sets from clinical settings
consisting of several thousands of samples): while it is easier to control
for high-quality data acquisition in small-scale experiments, typically run
in one or few batches, clinical data sets are often acquired over longer
time frames and are prone to higher technical variation that is often
unnoticed. MsQuality tries to address this problem by calculating metrics that
can be stored along the spectral data sets (raw files or feature-extracted
data sets). MsQuality, thus, facilitates the tracking of shifts in data quality
and quantifies the quality using multiple metrics. It should be thus easier
to identify samples that are of low quality (high-number of missing values,
termination of chromatographic runs, low instrument sensitivity, etc.).
The MsQuality package allows to calculate low-level quality metrics that require
minimum information on mass spectrometry data: retention time, m/z values,
and associated intensities.
The list included in the mzQC framework is excessive, also including
metrics that rely on more high-level information, that might not be readily
accessible from .raw or .mzML files, e.g. pump pressure mean, or rely
on alignment results, e.g. retention time mean shift, signal-to-noise ratio,
precursor errors (ppm).
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.
Contact
You are welcome to
- write a mail to
- submit suggestions and issues: https://github.com/tnaake/MsQuality/issues
- send a pull request: https://github.com/tnaake/MsQuality/issues
Install
MsQuality is available via Bioconductor. To install the package, users can
either install from the
devel branch
or from the current
RELEASE branch.
To install MsQuality, you have first to install the
BiocManager and
remotes
package:
```r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes") ```
Install the MsQuality package then via
```r
to install from Bioconductor
BiocManager::install("MsQuality")
to install the development version from GitHub
BiocManager::install("tnaake/MsQuality") ```
Owner
- Name: Thomas Naake
- Login: tnaake
- Kind: user
- Location: Hamburg, Germany
- Company: European Molecular Biology Laboratory (EMBL)
- Website: tnaake.github.io
- Repositories: 33
- Profile: https://github.com/tnaake
GitHub Events
Total
- Push event: 35
- Create event: 2
Last Year
- Push event: 35
- Create event: 2
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 10
- Total pull requests: 7
- Average time to close issues: 4 months
- Average time to close pull requests: 18 days
- Total issue authors: 3
- Total pull request authors: 1
- Average comments per issue: 2.2
- Average comments per pull request: 1.0
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- tnaake (7)
- jorainer (2)
- witszymanski (1)
Pull Request Authors
- jorainer (7)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 5,857 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 8
- Total maintainers: 1
bioconductor.org: MsQuality
MsQuality - Quality metric calculation from Spectra and MsExperiment objects
- Homepage: https://www.github.com/tnaake/MsQuality/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/MsQuality/inst/doc/MsQuality.pdf
- License: GPL-3
-
Latest release: 1.8.3
published 6 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.1.0 depends
- MsExperiment >= 0.6.1 imports
- ProtGenerics >= 1.24.0 imports
- Spectra >= 1.2.0 imports
- ggplot2 >= 3.3.5 imports
- htmlwidgets >= 1.5.3 imports
- methods >= 4.1.0 imports
- plotly >= 4.9.4.1 imports
- shiny >= 1.6.0 imports
- shinydashboard >= 0.7.1 imports
- stringr >= 1.4.0 imports
- tibble >= 3.1.4 imports
- tidyr >= 1.1.3 imports
- BiocGenerics >= 0.24.0 suggests
- BiocStyle >= 2.6.1 suggests
- S4Vectors >= 0.29.17 suggests
- dplyr >= 1.0.5 suggests
- knitr >= 1.11 suggests
- msdata >= 0.32.0 suggests
- rmarkdown >= 2.7 suggests
- testthat >= 2.2.1 suggests
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- docker/build-push-action v1 composite
- r-lib/actions/setup-pandoc v2-branch composite
- r-lib/actions/setup-r v2-branch composite