ProtGenerics
S4 generic functions for Bioconductor mass spectrometry infrastructure
Science Score: 36.0%
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Keywords
bioconductor
mass-spectrometry
metabolomics
proteomics
r
Keywords from Contributors
bioconductor-package
genomics
gene
feature-detection
peak-detection
proteomexchange
proteomics-data
spatial-proteomics
visualisation
core-package
Last synced: 6 months ago
·
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Repository
S4 generic functions for Bioconductor mass spectrometry infrastructure
Basic Info
Statistics
- Stars: 8
- Watchers: 3
- Forks: 6
- Open Issues: 1
- Releases: 0
Topics
bioconductor
mass-spectrometry
metabolomics
proteomics
r
Created about 11 years ago
· Last pushed 7 months ago
Metadata Files
Readme
Changelog
README.Rmd
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
fig.path = "README-"
)
```
# Generic infrastructure for Bioconductor mass spectrometry packages
## Description:
These generic functions and classes provide basic interfaces to
operations on and data access to mass spectrometry infrastructure in
the Bioconductor project.
For the details, please consult the respective methods' manual pages.
## Usage:
```r
psms(object, ...)
peaks(object, ...)
modifications(object, ...)
database(object, ...)
rtime(object, ...)
tic(object, ...)
spectra(object, ...)
intensity(object, ...)
mz(object, ...)
peptides(object, ...)
proteins(object, ...)
accessions(object, ...)
scans(object, ...)
mass(object, ...)
ions(object, ...)
chromatograms(object, ...)
chromatogram(object, ...)
isCentroided(object, ...)
## and many more - see below
```
## Arguments:
- `object`: Object of class for which methods are defined.
- `...`: Further arguments, possibly used by downstream methods.
## Details:
### When should one define a generics?:
Generics are appropriate for functions that have _generic_
names, i.e. names that occur in multiple circumstances, (with
different input classes, most often defined in different
packages) or, when (multiple) dispatching is better handled by
the generics mechanism rather than the developer. The
dispatching mechanism will then automatically call the
appropriate method and save the user from explicitly calling
`package::method` or the developer to handle the multiple input
types cases. When no such conflict exists or is unlikely to
happen (for example when the name of the function is specific to
a package or domain, or for class slots accessors and
replacement methods), the usage of a generic is arguably
questionable, and in most of these cases, simple,
straightforward functions would be perfectly valid.
### When to define a generic in `ProtGenerics`?:
`ProtGenerics` is not meant to be the central package for generics,
nor should it stop developers from defining the generics they need. It
is a means to centralise generics that are defined in different
packages (for example `mzR::psms` and `mzID::psms`, or
`IRanges::score` and `mzR::score`, now `BioGenerics::score`) or
generics that live in a rather big package (say `mzR`) on which one
wouldn't want to depend just for the sake of that generics'
definition.
The goal of `ProtGenerics` is to step in when namespace conflicts
arise so as to to facilitate inter-operability of packages. In case
such conflict appears due to multiple generics, we would (1) add these
same definitions in `ProtGenerics`, (2) remove the definitions from
the packages they stem from, which then (3) only need to import
`ProtGenerics`. This would be very minor/straightforward changes for
the developers and would resolve issues when they arise.
More generics can be added on request by opening an issue or sending a
pull request on:
[https://github.com/RforMassSpectrometry/ProtGenerics](https://github.com/RforMassSpectrometry/ProtGenerics)
## See Also:
- The `BiocGenerics` package for S4 generic functions needed by many
Bioconductor packages.
- `showMethods` for displaying a summary of the methods defined for a
given generic function.
- `selectMethod` for getting the definition of a specific method.
- `setGeneric` and `setMethod` for defining generics and methods.
## Examples:
```{r}
library("ProtGenerics")
## List all the symbols defined in this package:
ls('package:ProtGenerics')
library("mzR")
## What methods exists for 'peaks'
showMethods("peaks")
## To look at one method in particular
getMethod("peaks", "mzRpwiz")
```
Owner
- Name: RforMassSpectrometry
- Login: rformassspectrometry
- Kind: organization
- Email: maintainer@rformassspectrometry.org
- Website: https://www.rformassspectrometry.org/
- Repositories: 33
- Profile: https://github.com/rformassspectrometry
R packages for mass spectrometry
GitHub Events
Total
- Watch event: 1
- Push event: 5
- Pull request event: 2
- Create event: 1
Last Year
- Watch event: 1
- Push event: 5
- Pull request event: 2
- Create event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Laurent Gatto | l****o@u****e | 30 |
| Laurent | l****0@c****k | 27 |
| jorainer | j****r@g****m | 23 |
| Laurent Gatto | l****o@d****e | 21 |
| Nitesh Turaga | n****a@g****m | 14 |
| J Wokaty | j****y@s****u | 10 |
| Dan Tenenbaum | d****a@f****g | 6 |
| Herve Pages | h****s@f****g | 4 |
| vobencha | v****a@g****m | 2 |
| Philippine Louail | 1****l | 2 |
| Hervé Pagès | h****s@f****g | 2 |
| vobencha | v****n@r****g | 2 |
| Bioconductor Git-SVN Bridge | b****c@b****g | 2 |
| Sonali Arora | s****a@f****g | 1 |
Committer Domains (Top 20 + Academic)
fhcrc.org: 3
bioconductor.org: 1
roswellpark.org: 1
fredhutch.org: 1
sph.cuny.edu: 1
dnavision.be: 1
cam.ac.uk: 1
uclouvain.be: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 5
- Total pull requests: 19
- Average time to close issues: about 1 month
- Average time to close pull requests: 4 days
- Total issue authors: 2
- Total pull request authors: 4
- Average comments per issue: 2.2
- Average comments per pull request: 1.11
- Merged pull requests: 16
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: 42 minutes
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- lgatto (4)
- biodan25 (1)
Pull Request Authors
- jorainer (20)
- philouail (2)
- thomasp85 (2)
- sgibb (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 1,238,789 total
- Total dependent packages: 20
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: ProtGenerics
Generic infrastructure for Bioconductor mass spectrometry packages
- Homepage: https://github.com/RforMassSpectrometry/ProtGenerics
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/ProtGenerics/inst/doc/ProtGenerics.pdf
- License: Artistic-2.0
-
Latest release: 1.40.0
published 10 months ago
Rankings
Dependent repos count: 0.0%
Downloads: 2.6%
Dependent packages count: 3.2%
Average: 7.0%
Forks count: 11.0%
Stargazers count: 18.1%
Maintainers (1)
Last synced:
7 months ago
Dependencies
DESCRIPTION
cran
- methods * depends
- testthat * suggests