Package: gpmapr 0.0.1.0

Gibran Hemani

gpmapr: Query the OpenGWAS genotype-phenotype map

This package is a simple wrapper around the OpenGWAS genotype-phenotype map API.

Authors:Gibran Hemani [aut, cre]

gpmapr_0.0.1.0.tar.gz
gpmapr_0.0.1.0.zip(r-4.7)gpmapr_0.0.1.0.zip(r-4.6)gpmapr_0.0.1.0.zip(r-4.5)
gpmapr_0.0.1.0.tgz(r-4.6-any)gpmapr_0.0.1.0.tgz(r-4.5-any)
gpmapr_0.0.1.0.tar.gz(r-4.7-any)gpmapr_0.0.1.0.tar.gz(r-4.6-any)
gpmapr_0.0.1.0.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

On CRAN:

Conda:

5.84 score 6 stars 15 scripts 18 exports 37 dependencies

Last updated from:772eb97935. Checks:5 NOTE, 2 OK, 1 ERROR, 1 WARNING. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE205
source / vignettesOK657
linux-release-x86_64NOTE192
macos-release-arm64NOTE104
macos-oldrel-arm64ERROR101
windows-develWARNING128
windows-releaseNOTE117
windows-oldrelNOTE115
wasm-releaseOK138

Exports:all_genesall_traitsassociationsgenegenesget_all_gene_pleiotropiesget_all_variant_pleiotropiesget_gwashealth_apild_matrixld_proxiesregionsearch_gpmaptraittraitsupload_gwasvariantvariants

Dependencies:askpassbitbit64clicliprcpp11crayoncurldplyrgenericsgluehmshttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigprettyunitsprogresspurrrR6readrrlangstringistringrsystibbletidyrtidyselecttzdbutf8vctrsvroomwithr

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
Rendered fromgpmapr.Rmdusingknitr::rmarkdown

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
Rendered fromtutorial-case-study.Rmdusingknitr::rmarkdown

Last update: 2026-04-09
Started: 2026-03-26

GPMap tutorial: GWAS upload
Uploading a GWAS | Fetching your results | Interpreting your results | Study extractions | Coloc groups and coloc pairs
Rendered fromtutorial-gwas-upload.Rmdusingknitr::rmarkdown

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

Choosing Instrumental Variables tutorial
Rendered fromtutorial-choosing-ivs.Rmdusingknitr::rmarkdown

Last update: 2026-03-04
Started: 2026-03-04

Index of suspicion tutorial
Rendered fromtutorial-ios.Rmdusingknitr::rmarkdown

Last update: 2026-03-04
Started: 2025-05-07

Tissue stratification tutorial
Rendered fromtutorial-tissue-stratification.Rmdusingknitr::rmarkdown

Last update: 2026-03-04
Started: 2025-05-07

Trait clustering tutorial
Rendered fromtutorial-trait-clustering.Rmdusingknitr::rmarkdown

Last update: 2026-03-04
Started: 2025-05-07

Trait comparison tutorial
Rendered fromtutorial-trait-comparison.Rmdusingknitr::rmarkdown

Last update: 2026-03-04
Started: 2026-03-04

Readme and manuals

Help Manual

Help pageTopics
All genesall_genes
All traitsall_traits
Get Associations by SNP ID and Study IDassociations
Genegene
Genesgenes
Get All Gene Pleiotropiesget_all_gene_pleiotropies
Get All SNP Pleiotropiesget_all_variant_pleiotropies
Get a GWAS from the APIget_gwas
Get API Healthhealth_api
LD Matrixld_matrix
LD Proxiesld_proxies
Regionregion
Search the Genotype-Phenotype Mapsearch_gpmap
Traittrait
Traitstraits
Upload a GWAS to the APIupload_gwas
Variantvariant
Variantsvariants