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:Leqi Tian [aut], Tianwei Yu [aut], Tianwei Yu [cre]

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# Install 'metapone' in R:
install.packages('metapone', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • 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

4.00 score 9 scripts 217 downloads 5 exports 52 dependencies

Last updated 5 months agofrom:9fe5c68b6f. Checks:4 OK, 5 NOTE. Indexed: yes.

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Exports:bbplot1dbbplot2dftablemetaponeptable

Dependencies:BHBiocParallelclicodetoolscolorspacecommonmarkcowplotcpp11data.tabledotCall64fansifarverfastmatchfdrtoolfgseafieldsformatRfutile.loggerfutile.optionsggplot2ggrepelgluegtableisobandlabelinglambda.rlatticelifecyclelitedownmagrittrmapsmarkdownMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerRcpprlangscalessnowspamtibbleutf8vctrsviridisLitewithrxfun

METAbolic pathway testing combining POsitive and NEgative mode data (metapone)

Rendered frommetapone.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2022-06-04
Started: 2022-01-17