Uploading a GWAS | Fetching your results | Interpreting your results | Study extractions | Coloc groups and coloc pairs | Deleting an upload
Package: gpmapr 0.0.2.0
Gibran Hemani
gpmapr: Query the OpenGWAS genotype-phenotype map
This package is a simple wrapper around the OpenGWAS genotype-phenotype map API.
Authors:
gpmapr_0.0.2.0.tar.gz
gpmapr_0.0.2.0.zip(r-4.7-any)gpmapr_0.0.2.0.zip(r-4.6-any)gpmapr_0.0.2.0.zip(r-4.5-any)
gpmapr_0.0.2.0.tgz(r-4.6-any)gpmapr_0.0.2.0.tgz(r-4.5-any)
gpmapr_0.0.2.0.tar.gz(r-4.7-any)gpmapr_0.0.2.0.tar.gz(r-4.6-any)
gpmapr_0.0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
gpmapr/json (API)
| # Install 'gpmapr' in R: |
| install.packages('gpmapr', repos = c('https://mrcieu.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mrcieu/gpmapr/issues
Last updated from:ec12a1414e. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | NOTE | 164 | ||
| source / vignettes | OK | 790 | ||
| linux-release | NOTE | 157 | ||
| macos-release | NOTE | 111 | ||
| macos-oldrel | NOTE | 154 | ||
| windows-devel | NOTE | 112 | ||
| windows-release | NOTE | 110 | ||
| windows-oldrel | NOTE | 108 | ||
| wasm-release | OK | 105 |
Exports:all_genesall_traitsassociationsdelete_gwasgenegenesget_all_gene_pleiotropiesget_all_variant_pleiotropiesget_gwashealth_apild_matrixld_proxiesregionsearch_gpmaptraittrait_duplicatestraitsupload_gwasvariantvariants
Dependencies:askpassbitbit64clicliprcpp11crayoncurldplyrgenericsgluehmshttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigprettyunitsprogresspurrrR6readrrlangstringistringrsystibbletidyrtidyselecttzdbutf8vctrsvroomwithr
GPMap tutorial: GWAS upload
Last update: 2026-10-09
Started: 2026-03-26
Using gpmapr
Introduction | Getting started | Understanding info | Variant search returns proxy variants | Diving in | Trait example | How study_extractions, coloc_groups, and rare_results relate | Gene example | Coloc pairs example | Target–indication prioritisation workflow: Alzheimer's disease | Step 1: Genes mapped to Alzheimer's disease | Step 2: Rank by gene-level pleiotropy | Step 3: Variant-level specificity and consistency across variants and rare results | Diving deeper: TREM2 | Putting it together | Accessing summary statistics
Last update: 2026-05-13
Started: 2025-08-07
GPMap tutorial: Haemoglobin concentration case study
Trait colocalisations | Genome view | Complex trait colocalisations | Investigating a specific colocalisation group | TMPRSS6: eQTL/mQTL/sQTL and physiological measures | Region plot: scaled LBF values across all studies in the coloc group | Trait clustering
Last update: 2026-04-09
Started: 2026-03-26
Choosing Instrumental Variables tutorial
Last update: 2026-03-04
Started: 2026-03-04
Index of suspicion tutorial
Last update: 2026-03-04
Started: 2025-05-07
Tissue stratification tutorial
Last update: 2026-03-04
Started: 2025-05-07
Trait clustering tutorial
Last update: 2026-03-04
Started: 2025-05-07
Trait comparison tutorial
Last update: 2026-03-04
Started: 2026-03-04
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| All genes | all_genes |
| All traits | all_traits |
| Get Associations by SNP ID and Study ID | associations |
| Delete a GWAS upload | delete_gwas |
| Gene | gene |
| Genes | genes |
| Get All Gene Pleiotropies | get_all_gene_pleiotropies |
| Get All SNP Pleiotropies | get_all_variant_pleiotropies |
| Get a GWAS from the API | get_gwas |
| Get API Health | health_api |
| LD Matrix | ld_matrix |
| LD Proxies | ld_proxies |
| Region | region |
| Search the Genotype-Phenotype Map | search_gpmap |
| Trait | trait |
| Trait duplicates | trait_duplicates |
| Traits | traits |
| Upload a GWAS to the API | upload_gwas |
| Variant | variant |
| Variants | variants |