GWAS across all analyzable phenotypes and diverse ancestry groups in the UK Biobank.
A full description of how these summary statistics were generated and how to work with them can be found here: http://pan.ukbb.broadinstitute.org/.
The code in this repo can be used to generate all the figures in the manuscript. They look for data files in ./data, and if they are not found, downloads them as needed from the public data repository.
Each figure panel can be generated individually, or figures as a whole. For instance, in R/fig3_spectrum.R, we provide a function called figure3() which can generate the entirety of figure 3. Alternatively, running the code inside the function can generate each figure panel separately. Note that for some figures, on some R setups, attempting to generate the full figure by calling the function directly can crash R: we are uncertain of the cause of the issue, but it can be resolved by running the code inside the function step-wise.
There are no specific hardware requirements, except enough RAM to fit the datasets in memory (~16Gb).
This package has been tested on macOS Sonoma (14.5).
The code depends on R packages, including those listed at the top of constants.R, using R 4.3.3 (sessionInfo() used below).
git clone https://github.com/atgu/ukbb_pan_ancestry
cd ukbb_pan_ancestry
R
- Install any packages needed, and run
constants.R- if this runs without error, the remaining files will load.
To cite the Pan-UKB resource, please use the citation: Karczewski, Gupta, Kanai et al., 2024.
> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin23.2.0 (64-bit)
Running under: macOS Sonoma 14.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] googlesheets4_1.1.1 colorspace_2.1-0 reticulate_1.35.0 magick_2.8.1 png_0.1-8
[6] IsoplotR_5.6 ggpmisc_0.6.0 ggpp_0.5.8-1 ggbreak_0.1.2 ggthemes_5.0.0
[11] ggwordcloud_0.6.1 cowplot_1.1.1 RMySQL_0.10.27 DBI_1.1.3 ggrepel_0.9.4
[16] pbapply_1.7-2 rlang_1.1.4 tidygraph_1.3.1 meta_6.5-0 ggrastr_1.0.2
[21] ggpubr_0.6.0 ggridges_0.5.4 readxl_1.4.3 corrr_0.4.4 corrplot_0.92
[26] patchwork_1.1.3.9000 naniar_1.0.0 plotROC_2.3.1 gghighlight_0.4.0 skimr_2.1.5
[31] gapminder_1.0.0 trelliscopejs_0.2.10 scales_1.3.0 magrittr_2.0.3 slackr_3.3.1
[36] plotly_4.10.3 broom_1.0.5 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[41] dplyr_1.1.4 purrr_1.0.2 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
[46] ggplot2_3.5.1 tidyverse_2.0.0 plyr_1.8.9 RCurl_1.98-1.16 Hmisc_5.1-1
loaded via a namespace (and not attached):
[1] splines_4.3.3 bitops_1.0-7 ggplotify_0.1.2 locusviz_0.1.0
[5] cellranger_1.1.0 rpart_4.1.21 lifecycle_1.0.4 rstatix_0.7.2
[9] doParallel_1.0.17 vroom_1.6.4 lattice_0.22-5 MASS_7.3-60
[13] backports_1.4.1 metafor_4.4-0 rmarkdown_2.25 minqa_1.2.6
[17] RColorBrewer_1.1-3 abind_1.4-5 fidelius_0.0.2 BiocGenerics_0.48.1
[21] yulab.utils_0.1.0 nnet_7.3-19 circlize_0.4.15 IRanges_2.36.0
[25] S4Vectors_0.40.2 MatrixModels_0.5-3 codetools_0.2-19 xml2_1.3.6
[29] tidyselect_1.2.0 shape_1.4.6 aplot_0.2.2 farver_2.1.1
[33] lme4_1.1-35.1 matrixStats_1.1.0 stats4_4.3.3 base64enc_0.1-3
[37] googledrive_2.1.1 webshot_0.5.5 mathjaxr_1.6-0 jsonlite_1.8.8
[41] GetoptLong_1.0.5 Formula_1.2-5 survival_3.5-7 iterators_1.0.14
[45] foreach_1.5.2 tools_4.3.3 progress_1.2.2 Rcpp_1.0.11
[49] glue_1.6.2 gridExtra_2.3 xfun_0.41 withr_2.5.2
[53] numDeriv_2016.8-1.1 fastmap_1.1.1 boot_1.3-28.1 fansi_1.0.5
[57] SparseM_1.81 digest_0.6.33 timechange_0.2.0 R6_2.5.1
[61] gridGraphics_0.5-1 visdat_0.6.0 scattermore_1.2 utf8_1.2.4
[65] generics_0.1.3 data.table_1.14.8 prettyunits_1.2.0 httr_1.4.7
[69] htmlwidgets_1.6.3 pkgconfig_2.0.3 gtable_0.3.4 ComplexHeatmap_2.18.0
[73] htmltools_0.5.7 carData_3.0-5 autocogs_0.1.4 clue_0.3-65
[77] ggfun_0.1.3 knitr_1.45 rstudioapi_0.15.0 tzdb_0.4.0
[81] rjson_0.2.21 curl_5.1.0 checkmate_2.3.1 nlme_3.1-164
[85] nloptr_2.0.3 repr_1.1.6 cachem_1.0.8 GlobalOptions_0.1.2
[89] parallel_4.3.3 vipor_0.4.5 metadat_1.2-0 foreign_0.8-86
[93] pillar_1.9.0 vctrs_0.6.5 car_3.1-2 cluster_2.1.6
[97] beeswarm_0.4.0 htmlTable_2.4.2 evaluate_0.23 cli_3.6.1
[101] compiler_4.3.3 crayon_1.5.2 ggsignif_0.6.4 labeling_0.4.3
[105] mclust_6.0.1 fs_1.6.3 ggbeeswarm_0.7.2 stringi_1.8.4
[109] viridisLite_0.4.2 munsell_0.5.0 lazyeval_0.2.2 CompQuadForm_1.4.3
[113] quantreg_5.97 Matrix_1.6-4 hms_1.1.3 bit64_4.0.5
[117] gridtext_0.1.5 gargle_1.5.2 igraph_2.0.3 memoise_2.0.1
[121] bit_4.0.5 DistributionUtils_0.6-1 polynom_1.4-1