Package: gpmapr 1.0.0

Andrew Elmore

gpmapr: Query the 'OpenGWAS' Genotype-Phenotype Map

Client for the 'OpenGWAS' genotype-phenotype map ('GPMap') API <https://gpmap.opengwas.io>, which brings together colocalisation, rare variant and molecular QTL results across thousands of traits. Functions retrieve traits, genes, variants and genomic regions with their colocalising studies, associations, linkage disequilibrium and pleiotropy summaries, search the map by name or variant, and upload GWAS summary statistics for analysis against it.

Authors:Andrew Elmore [aut, cre], Gibran Hemani [aut]

gpmapr_1.0.0.tar.gz
gpmapr_1.0.0.zip(r-4.7-any)gpmapr_1.0.0.zip(r-4.6-any)gpmapr_1.0.0.zip(r-4.5-any)
gpmapr_1.0.0.tgz(r-4.6-any)gpmapr_1.0.0.tgz(r-4.5-any)
gpmapr_1.0.0.tar.gz(r-4.7-any)gpmapr_1.0.0.tar.gz(r-4.6-any)
gpmapr_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
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

On CRAN:

Conda:

5.39 score 6 stars 18 scripts 22 exports 33 dependencies

Last updated from:a571229c9d. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK175
source / vignettesOK178
linux-releaseOK195
macos-releaseOK165
macos-oldrelOK169
windows-develOK144
windows-releaseOK115
windows-oldrelOK131
wasm-releaseOK109

Exports:all_genesall_traitsassociationscompare_uploaddelete_gwasgenegenesget_all_gene_pleiotropiesget_all_variant_pleiotropiesget_gwasgpmap_availablehealth_apild_matrixld_proxiesregionsearch_gpmaptraittrait_duplicatestraitsupload_gwasvariantvariants

Dependencies:askpassbitbit64clicliprcpp11crayoncurldplyrgenericsgluehmshttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigprettyunitsprogressR6readrrlangsystibbletidyselecttzdbutf8vctrsvroomwithr

Getting started with 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
Rendered fromgpmapr.Rmdusingknitr::rmarkdown

Last update: 2026-10-23
Started: 2025-08-07

GPMap tutorial: GWAS upload
Uploading a GWAS | Fetching your results | Interpreting your results | Your upload's rows and everyone else's | Comparing your upload with another trait | Deleting an upload
Rendered fromtutorial-gwas-upload.Rmdusingknitr::rmarkdown

Last update: 2026-10-23
Started: 2026-03-26

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
Rendered fromtutorial-case-study.Rmdusingknitr::rmarkdown

Last update: 2026-10-23
Started: 2026-03-26