Script dependencies NESDA server.R
Script GE Analysis.R
Script data cleaning.R
Script dependencies.R
Script Clump Plink.R
Script FUMA Results.R
Script SuppData Descriptives.R
plink_clump.sh
plink_clump_newdata.sh
plink_clump_all.sh
plink_clump_all_newdata.sh
plink_ld_calc.sh
plink_ld_calc_newdata.sh
plink_ld_calc_all.sh
plink_ld_calc_all_newdata.sh
fig_hist_circ.R
gantt_chart.R
venn_diagram.R
R and Rstudios were used for main analyses regarding the regression models. FUMA-software was used for single level gene analyses, providing overrepresentation in sets of differentially expressed genes, and hypergeometric tests. Plink 2 and Unix shell scripts were used for eQTL analyses. For a full overview of the Unix shell- and R-scripts used, see github.
For our analyses in R, we used R (Version 4.0.4, R Core Team, 2021) and the R-packages anytime (Version 0.3.9, Eddelbuettel, 2020), cowplot (Version 1.1.1, Wilke, 2020), data.table (Version 1.14.0, Dowle & Srinivasan, 2021), dplyr (Version 1.0.6, Wickham, François, Henry, & Müller, 2021), forcats (Version 0.5.1, Wickham, 2021a), gee (Version 4.13.20, R by Thomas Lumley & Ripley., 2019), ggplot2 (Version 3.3.4, Wickham, 2016), haven (Version 2.4.1, Wickham & Miller, 2021), kableExtra (Version 1.3.4, Zhu, 2021), lubridate (Version 1.7.10, Grolemund & Wickham, 2011), metap (Version 1.4, Dewey, 2020), openxlsx (Version 4.2.4, Schauberger & Walker, 2021), papaja (Version 0.1.0.9997, Aust & Barth, 2020), psych (Version 2.1.6, Revelle, 2021), purrr (Version 0.3.4, Henry & Wickham, 2020), readr (Version 1.4.0, Wickham & Hester, 2020), readxl (Version 1.3.1, Wickham & Bryan, 2019), reshape2 (Version 1.4.4, Wickham, 2007), scales (Version 1.1.1, Wickham & Seidel, 2020), stringr (Version 1.4.0, Wickham, 2019), tibble (Version 3.1.2, Müller & Wickham, 2021), tidyr (Version 1.1.3, Wickham, 2021b), and tidyverse (Version 1.3.1, Wickham et al., 2019).
Watanabe, K., Taskesen, E., Bochoven, A. van, & Posthuma, D. (2017). Functional mapping and annotation of genetic associations with FUMA. Nature Communications, 8 (1), 1826. https://doi.org/10.1038/s41467-017-01261-5
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D.,... Sham, P. C. (2007). PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. The American Journal of Human Genetics, 81 (3), 559–575. https://doi.org/10.1086/519795
Aust, F., & Barth, M. (2020). papaja: Create APA manuscripts with R Markdown. Retrieved from https://github.com/crsh/papaja
Dewey, M. (2020). metap: Meta-analysis of significance values.
Dowle, M., & Srinivasan, A. (2021). Data.table: Extension of ‘data.frame‘. Retrieved from https://CRAN.R-project.org/package=data.table
Eddelbuettel, D. (2020). Anytime: Anything to ’POSIXct’ or ’date’ converter. Retrieved from https://CRAN.R-project.org/package=anytime
Grolemund, G., & Wickham, H. (2011). Dates and times made easy with lubridate. Journal of Statistical Software, 40 (3), 1–25. Retrieved from https://www.jstatsoft.org/v40/i03/
Henry, L., & Wickham, H. (2020). Purrr: Functional programming tools. Retrieved from https://CRAN.R-project.org/package=purrr
Müller, K., & Wickham, H. (2021). Tibble: Simple data frames. Retrieved from https://CRAN.R-project.org/package=tibble
R by Thomas Lumley, V. J. Carey. P. to, & Ripley., B. (2019). Gee: Generalized estimation equation solver. Retrieved from https://CRAN.R-project.org/package=gee
R Core Team. (2021). R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. Retrieved from https://www.R-project.org/
Revelle, W. (2021). Psych: Procedures for psychological, psychometric, and personality research. Evanston, Illinois: Northwestern University. Retrieved from https://CRAN.R-project.org/package=psych
Schauberger, P., & Walker, A. (2021). Openxlsx: Read, write and edit xlsx files. Retrieved from https://CRAN.R-project.org/package=openxlsx
Wickham, H. (2007). Reshaping data with the reshape package. Journal of Statistical Software, 21 (12), 1–20. Retrieved from http://www.jstatsoft.org/v21/i12/
Wickham, H. (2016). ggplot2: Elegant graphics for data analysis. Springer-Verlag New York. Retrieved from https://ggplot2.tidyverse.org
Wickham, H. (2019). Stringr: Simple, consistent wrappers for common string operations. Retrieved from https://CRAN.R-project.org/package=stringr
Wickham, H. (2021a). Forcats: Tools for working with categorical variables (factors). Retrieved from https://CRAN.R-project.org/package=forcats
Wickham, H. (2021b). Tidyr: Tidy messy data. Retrieved from https://CRAN.R-project.org/package=tidyr
Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L. D., François, R., . . . Yutani, H. (2019). Welcome to the tidyverse. Journal of Open Source Software, 4 (43), 1686. https://doi.org/10.21105/joss.01686
Wickham, H., & Bryan, J. (2019). Readxl: Read excel files. Retrieved from https://CRAN.R-project.org/package=readxl
Wickham, H., François, R., Henry, L., & Müller, K. (2021). Dplyr: A grammar of data manipulation. Retrieved from https://CRAN.R-project.org/package=dplyr
Wickham, H., & Hester, J. (2020). Readr: Read rectangular text data. Retrieved from https://CRAN.R-project.org/package=readr
Wickham, H., & Miller, E. (2021). Haven: Import and export ’SPSS’, ’stata’ and ’SAS’ files. Retrieved from https://CRAN.R-project.org/package=haven
Wickham, H., & Seidel, D. (2020). Scales: Scale functions for visualization. Retrieved from https://CRAN.R-project.org/package=scales
Wilke, C. O. (2020). Cowplot: Streamlined plot theme and plot annotations for ’ggplot2’. Retrieved from https://CRAN.R-project.org/package=cowplot
Zhu, H. (2021). kableExtra: Construct complex table with ’kable’ and pipe syntax. Retrieved from https://CRAN.R-project.org/package=kableExtra