Package: gwasglue 0.0.0.9000

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]

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gwasglue.pdf |gwasglue.html✨
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:

4.64 score 113 stars 78 scripts 23 exports 188 dependencies

Last updated 3 years agofrom:c2d5660eed. Checks:ERROR: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Oct 25 2024
R-4.5-win	ERROR	Oct 25 2024
R-4.5-linux	ERROR	Oct 25 2024
R-4.4-win	ERROR	Oct 25 2024
R-4.4-mac	ERROR	Oct 25 2024
R-4.3-win	ERROR	Oct 25 2024
R-4.3-mac	ERROR	Oct 25 2024

Exports:%>%clump_gwasvcf cojo_cond cojo_sumstat_file coloc_to_gassocplot gwasvcf_to_coloc gwasvcf_to_finemapr gwasvcf_to_TwoSampleMR harmonise harmonise_against_ref ieugwasr_to_coloc ieugwasr_to_finemapr ieugwasr_to_gassocplot ieugwasr_to_TwoSampleMR is_forward_strand make_TwoSampleMR_dat map_variants_to_regions pwcoco read_gwas read_reference set_bc4_files susieR_pipeline write_out

Dependencies:abind AnnotationDbi arrangements askpass base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob boot brio BSgenome bslib cachem callr cli clipr codetools colorspace CompQuadForm cowplot cpp11 crayon crosstalk curl data.table DBI DelayedArray DEoptimR desc diffobj digest dplyr evaluate fansi farver fastmap fontawesome foreach formatR fs futile.logger futile.options generics genetics.binaRies GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glmnet glue gmp GPArotation gridExtra gtable gwasglue2 gwasvcf highr hms htmltools htmlwidgets httr ieugwasr IRanges irlba isoband iterators iterpc jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle lme4 magrittr MASS mathjaxr Matrix MatrixGenerics MatrixModels matrixStats memoise MendelianRandomization meta metadat metafor mgcv mime minqa mixsqp mnormt mr.raps MRMix MRPRESSO munsell nlme nloptr nortest numDeriv openssl pbapply pillar pkgbuild pkgconfig pkgload plogr plotly plyr png praise prettyunits processx progress promises ps psych purrr quantreg R6 RadialMR rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl readr rematch2 reshape reshape2 restfulr Rhtslib rjson rlang rmarkdown robustbase rprojroot Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass scales shape snow SparseArray SparseM stringi stringr SummarizedExperiment survival susieR sys testthat tibble tidyr tidyselect tinytex TwoSampleMR tzdb UCSC.utils utf8 VariantAnnotation vctrs viridisLite vroom waldo withr xfun XML xml2 XVector yaml zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Perform LD clumping	clump_gwasvcf
Perform conditional analysis using GCTA COJO	cojo_cond
Write vcf file to cojo sumstat file	cojo_sumstat_file
Convert coloc dataset to gassocplot dataset	coloc_to_gassocplot
Generate coloc dataset from vcf files	gwasvcf_to_coloc
Generate data for fine mapping analysis	gwasvcf_to_finemapr
Create exposure or outcome data format for TwoSampleMR from vcf	gwasvcf_to_TwoSampleMR
Generic harmonisation function	harmonise
Harmonise gwas alleles to be same as reference	harmonise_against_ref
Generate coloc dataset from the IEU GWAS database	ieugwasr_to_coloc
Generate data for analysis in various finemapping methods	ieugwasr_to_finemapr
Generate regional plot for ieugwasr	ieugwasr_to_gassocplot
Convert output from query to TwoSampleMR format	ieugwasr_to_TwoSampleMR
Check a GWAS dataset against a reference known to be on the forward strand	is_forward_strand
Create a harmonised dataset from lists of vcf files	make_TwoSampleMR_dat
For a set of variants map to LD regions	map_variants_to_regions
Figure out specific files and IDs depending on what files exist and whethet vcfdir is set	organise_ids
Read in GWAS dataset	read_gwas
Read in reference dataset	read_reference
Determine locations of useful reference datasets on bluecrystal4	set_bc4_files
Perform fine mapping pipeline using susieR	susieR_pipeline
Create format for HPC pipeline	write_out