Package: metapone 1.13.0
Tianwei Yu
metapone: Conducts pathway test of metabolomics data using a weighted permutation test
The package conducts pathway testing from untargetted metabolomics data. It requires the user to supply feature-level test results, from case-control testing, regression, or other suitable feature-level tests for the study design. Weights are given to metabolic features based on how many metabolites they could potentially match to. The package can combine positive and negative mode results in pathway tests.
Authors:
metapone_1.13.0.tar.gz
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metapone.pdf |metapone.html✨
metapone/json (API)
| # Install 'metapone' in R: |
| install.packages('metapone', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- hmdbCompMZ - The m/z values of common adduct ions of HMDB metaboites
- hmdbCompMZ.metapone - The m/z values of common adduct ions of metapone metaboites
- neg - Example negative mode data from the Metabolome Atlas of the Aging Mouse Brain
- pa - Pathway-metabolite match file.
- pos - Example positive mode data from the Metabolome Atlas of the Aging Mouse Brain
On BioConductor:metapone-1.13.0(bioc 3.21)metapone-1.12.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
technologymassspectrometrymetabolomicspathways
Last updated 2 months agofrom:9fe5c68b6f. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 01 2024 |
| R-4.5-win | OK | Dec 01 2024 |
| R-4.5-linux | OK | Dec 01 2024 |
| R-4.4-win | NOTE | Dec 01 2024 |
| R-4.4-mac | NOTE | Dec 01 2024 |
| R-4.3-win | NOTE | Dec 01 2024 |
| R-4.3-mac | NOTE | Dec 01 2024 |
Exports:bbplot1dbbplot2dftablemetaponeptable
Dependencies:BHBiocParallelclicodetoolscolorspacecommonmarkcowplotcpp11data.tabledotCall64fansifarverfastmatchfdrtoolfgseafieldsformatRfutile.loggerfutile.optionsggplot2ggrepelgluegtableisobandlabelinglambda.rlatticelifecyclemagrittrmapsmarkdownMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerRcpprlangscalessnowspamtibbleutf8vctrsviridisLitewithrxfun
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Conducts pathway test of metabolomics data using a weighted permutation test | metapone-package |
| Plot of metapone result. | bbplot1d |
| Plot of metapone result. | bbplot2d |
| Acessor functions for the feature mapping table in a metaponeResult object. | ftable ftable,metaponeResult-method |
| the m/z values of common adduct ions of HMDB metaboites | hmdbCompMZ |
| the m/z values of common adduct ions of metapone metaboites | hmdbCompMZ.metapone |
| METAbolic pathway testing using both POsitive and NEgative mode data | metapone |
| Class "metaponeResult" | ftable, metaponeResult-method metaponeResult metaponeResult-class metaponeResult-method ptable, metaponeResult-method |
| Example negative mode data from the Metabolome Atlas of the Aging Mouse Brain | neg |
| Pathway-metabolite match file. | pa |
| Example positive mode data from the Metabolome Atlas of the Aging Mouse Brain | pos |
| Acessor functions for the test result table in a metaponeResult object. | ptable ptable,metaponeResult-method |