Package: gwasglue 0.0.0.9001

Gibran Hemani

gwasglue: GWAS summary data sources connected to analytical tools

Many tools exist that use GWAS summary data for colocalisation, fine mapping, Mendelian randomization, visualisation, etc. This package is a conduit that connects R packages that can retrieve GWAS summary data to various tools for analysing those data.

Authors:Gibran Hemani [aut, cre]

gwasglue_0.0.0.9001.tar.gz
gwasglue_0.0.0.9001.zip(r-4.7)gwasglue_0.0.0.9001.zip(r-4.6)gwasglue_0.0.0.9001.zip(r-4.5)
gwasglue_0.0.0.9001.tgz(r-4.6-any)gwasglue_0.0.0.9001.tgz(r-4.5-any)
gwasglue_0.0.0.9001.tar.gz(r-4.7-any)gwasglue_0.0.0.9001.tar.gz(r-4.6-any)
gwasglue_0.0.0.9001.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
gwasglue/json (API)
NEWS

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

Bug tracker:https://github.com/mrcieu/gwasglue/issues

On CRAN:

Conda:

5.17 score 142 scripts 23 exports 144 dependencies

Last updated from:7fa098bfba (on fixes). Checks:7 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING190
source / vignettesOK341
linux-release-x86_64WARNING212
macos-release-arm64WARNING137
macos-oldrel-arm64WARNING122
windows-develWARNING125
windows-releaseWARNING170
windows-oldrelWARNING129
wasm-releaseOK176

Exports:%>%clump_gwasvcfcojo_condcojo_sumstat_filecoloc_to_gassocplotgwasvcf_to_colocgwasvcf_to_finemaprgwasvcf_to_TwoSampleMRharmoniseharmonise_against_refieugwasr_to_colocieugwasr_to_finemaprieugwasr_to_gassocplotieugwasr_to_TwoSampleMRis_forward_strandmake_TwoSampleMR_datmap_variants_to_regionspwcocoread_gwasread_referenceset_bc4_filessusieR_pipelinewrite_out

Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibcachemcigarilloclicodetoolscowplotcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdplyrevaluatefarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsgenetics.binaRiesGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2glmnetglueGPArotationgridExtragtablegwasglue2gwasvcfhighrhtmltoolshtmlwidgetshttrieugwasrIRangesirlbaisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimemixsqpmnormtMRMixMRPRESSOnlmeopensslotelpbapplypillarpkgconfigplotlyplyrpngpromisespsychpurrrR6RadialMRrappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreshapereshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sassscalesSeqinfoshapesnowSparseArraystringistringrSummarizedExperimentsurvivalsusieRsystibbletidyrtidyselecttinytexTwoSampleMRUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLXVectoryaml

Clumping and finemapping

Rendered fromfinemapping.Rmdusingknitr::rmarkdownon May 15 2026.

Last update: 2021-04-12
Started: 2019-11-06

Conditional analysis of VCF files

Rendered fromcojo.Rmdusingknitr::rmarkdownon May 15 2026.

Last update: 2020-07-09
Started: 2020-07-07

Finemapping experiments

Rendered fromfinemapping_experiment.Rmdusingknitr::rmarkdownon May 15 2026.

Last update: 2021-04-12
Started: 2021-04-12

Generate LD matrices

Rendered fromld_ref.Rmdusingknitr::rmarkdownon May 15 2026.

Last update: 2025-08-01
Started: 2021-02-24

Genetic colocalisation

Rendered fromcolocalisation.Rmdusingknitr::rmarkdownon May 15 2026.

Last update: 2025-08-01
Started: 2019-11-06

Major changes to the IEU GWAS resources for 2020

Rendered fromgwas2020.Rmdusingknitr::rmarkdownon May 15 2026.

Last update: 2020-01-11
Started: 2020-01-07

Mendelian randomization

Rendered frommr.Rmdusingknitr::rmarkdownon May 15 2026.

Last update: 2025-08-01
Started: 2019-11-06

Readme and manuals

Help Manual

Help pageTopics
Perform LD clumpingclump_gwasvcf
Perform conditional analysis using GCTA COJOcojo_cond
Write vcf file to cojo sumstat filecojo_sumstat_file
Convert coloc dataset to gassocplot datasetcoloc_to_gassocplot
Generate coloc dataset from vcf filesgwasvcf_to_coloc
Generate data for fine mapping analysisgwasvcf_to_finemapr
Write files for PWCoCo where data are read from two VCF objects or files.gwasvcf_to_pwcoco
Create exposure or outcome data format for TwoSampleMR from vcfgwasvcf_to_TwoSampleMR
Generic harmonisation functionharmonise
Harmonise gwas alleles to be same as referenceharmonise_against_ref
Generate coloc dataset from the IEU GWAS databaseieugwasr_to_coloc
Generate data for analysis in various finemapping methodsieugwasr_to_finemapr
Generate regional plot for ieugwasrieugwasr_to_gassocplot
Write files for PWCoCo where data are read from the OpenGWAS DB.ieugwasr_to_pwcoco
Convert output from query to TwoSampleMR formatieugwasr_to_TwoSampleMR
Check a GWAS dataset against a reference known to be on the forward strandis_forward_strand
Create a harmonised dataset from lists of vcf filesmake_TwoSampleMR_dat
For a set of variants map to LD regionsmap_variants_to_regions
Figure out specific files and IDs depending on what files exist and whethet vcfdir is setorganise_ids
Perform pair-wise conditional and colocalisation analysis using PWCoCopwcoco
Read in GWAS datasetread_gwas
Read in reference datasetread_reference
Determine locations of useful reference datasets on bluecrystal4set_bc4_files
Perform fine mapping pipeline using susieRsusieR_pipeline
Create format for HPC pipelinewrite_out