Introduction | Mini overview of magmaR, magma, and the UCSF Data Library system | Scope of this vignette | How magmaR functions work | Upload Functions | Overview | Common features | Running non-interactively | Example Data | Function Details | updateMatrix() | Necessary inputs: | updateFromDF() | updateValues() | Session information
Package: magmaR 1.0.4
magmaR: R-Client for Interacting with the 'UCSF Data Library'
A client for interacting with 'magma', the data warehouse of the 'UCSF Data Library'. 'magmaR' includes functions for querying and downloading data from 'magma', in order to enable working with such data in R, as well as for uploading local data to 'magma'.
Authors:
magmaR_1.0.4.tar.gz
magmaR_1.0.4.zip(r-4.7-any)magmaR_1.0.4.zip(r-4.6-any)magmaR_1.0.4.zip(r-4.5-any)
magmaR_1.0.4.tgz(r-4.6-any)magmaR_1.0.4.tgz(r-4.5-any)
magmaR_1.0.4.tar.gz(r-4.7-any)magmaR_1.0.4.tar.gz(r-4.6-any)
magmaR_1.0.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
magmaR/json (API)
| # Install 'magmaR' in R: |
| install.packages('magmaR', repos = c('https://dtm2451.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:0bcd938919. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 158 | ||
| source / vignettes | OK | 180 | ||
| linux-release | OK | 179 | ||
| macos-release | OK | 173 | ||
| macos-oldrel | OK | 169 | ||
| windows-devel | OK | 86 | ||
| windows-release | OK | 75 | ||
| windows-oldrel | OK | 78 | ||
| wasm-release | OK | 113 |
Exports:magmaRsetqueryretrieveretrieveAttributesretrieveIdsretrieveJSONretrieveMatrixretrieveMetadataretrieveModelsretrieveParentNameretrieveProjectsretrieveTemplateupdateFromDFupdateMatrixupdateValues
Dependencies:clicrulcurlhttpcodejsonlitelifecyclemimeR6Rcpprlangtriebeardurltools
Uploading data to magma with the R-client magmaR
Last update: 2025-05-23
Started: 2021-04-29
Downloading data from magma with the R-client magmaR
Quick Start | Introduction | magmaR, magma, and the UCSF Data Library | Organization of data within magma | How magmaR functions work | Data Restructuring Details | The two main output structures of magma returns | Installation | Authorization process, a.k.a. janus token utilization: | Providing a token | When magma thinks you are unauthorized | Controlling which version of magma to target | Helper functions | Main data download functions: | retrieve() & retrieveJSON() | retrieveMatrix() | query() | retrieveMetadata() | Putting it all together | Session information
Last update: 2024-01-25
Started: 2021-04-29
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Starting out and working with different Etna environments | authentication-and-environments |
| Set up your magma environment and authentication | magmaRset |
| Search-like function that can obtain linked data from distinct models. | query |
| Download data from magma as a tsv, and convert to a data.frame | retrieve |
| Helper functions that utilize special cases of magma /retrieve | retrieveAttributes retrieveIds retrieveModels retrieveParentName retrieveTemplate retrieve_SpecialCases |
| Download data from magma as a json, and convert to a list | retrieveJSON |
| Download data from magma that is stored as a matrix | retrieveMatrix |
| Download data from magma of one model, but transformed into the shape of a different model's records. | retrieveMetadata |
| Helper function that retrieves all the projectName options which a user has access to, from janus. | retrieveProjects |
| Easier to use wrapper of 'updateValues' | updateFromDF |
| A matrix-specific wrapper of 'updateValues' | updateMatrix |
| Analogous to the '/update' function of magma | updateValues |