Last updated: 2021-06-06

Checks: 7 0

Knit directory: rss-net-results/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

The command set.seed(20180719) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 098e537. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/

Unstaged changes:
    Modified:   analysis/_site.yml

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.


These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd 098e537 xiangzhu 2021-06-06 wflow_publish(“analysis/index.Rmd”)
html 2152ba0 xiangzhu 2020-12-02 Build site.
html 1cdcc7a xiangzhu 2020-11-30 Build site.
html a0ae50d xiangzhu 2020-11-30 Build site.
Rmd ea84102 xiangzhu 2020-11-30 wflow_publish(“analysis/index.Rmd”)
Rmd dad5e8d xiangzhu 2020-11-30 wflow_remove(“analysis/index.Rmd”)
html dad5e8d xiangzhu 2020-11-30 wflow_remove(“analysis/index.Rmd”)
html f40af1c xiangzhu 2020-11-30 Build site.
html 9874243 Xiang Zhu 2020-08-03 Build site.
html e553de6 Xiang Zhu 2020-06-02 Build site.
html 714d52a xiangzhu 2020-03-16 Build site.
Rmd 80bed5a xiangzhu 2020-03-16 wflow_publish(“analysis/index.Rmd”)
html de24221 xiangzhu 2020-03-15 Build site.
Rmd 7d637d3 xiangzhu 2020-03-15 wflow_publish(“analysis/index.Rmd”)
html 32f7990 xiangzhu 2020-03-15 Build site.
Rmd 74a11d4 xiangzhu 2020-03-15 wflow_publish(“analysis/index.Rmd”)
html 1537c9d xiangzhu 2020-03-08 Build site.
Rmd 5eb19aa xiangzhu 2020-03-08 wflow_publish(“analysis/index.Rmd”)
html 0a3163f xiangzhu 2020-03-08 Build site.
Rmd 9417e91 xiangzhu 2020-03-08 wflow_publish(“analysis/index.Rmd”)
html 8fde153 xiangzhu 2020-02-06 Build site.
html 8209433 xiangzhu 2020-01-31 Build site.
html 1373e08 xiangzhu 2019-11-30 Build site.
Rmd 40c91fa xiangzhu 2019-11-30 wflow_publish(“analysis/index.Rmd”)
html 752084c xiangzhu 2019-11-30 Build site.
html b359434 xiangzhu 2019-10-20 Build site.
Rmd 758982a xiangzhu 2019-10-20 wflow_publish(“analysis/index.Rmd”)
html b526deb xiangzhu 2019-09-30 Build site.
html 4ce20ab xiangzhu 2019-09-30 Build site.
html 1fc5763 xiangzhu 2019-09-30 Build site.
html 4132873 xiangzhu 2019-09-18 Build site.
html b2953b2 xiangzhu 2019-09-14 Build site.
html bda261e xiangzhu 2019-09-09 Build site.
html 2c63955 xiangzhu 2019-09-05 Build site.
html 9e90b1a xiangzhu 2019-08-27 Build site.
html a86ad3e xiangzhu 2019-08-22 Build site.
html 954ffa5 xiangzhu 2019-08-20 Build site.
Rmd 1a85c20 xiangzhu 2019-08-20 wflow_publish(“analysis/index.Rmd”)
html 9660674 xiangzhu 2019-08-19 Build site.
Rmd 883bf45 xiangzhu 2019-08-19 wflow_publish(“analysis/index.Rmd”)
html a13ed62 xiangzhu 2019-08-17 Build site.
Rmd aa4cbe0 xiangzhu 2019-08-17 wflow_publish(“analysis/index.Rmd”)
html 0765177 Xiang Zhu 2018-10-10 Build site.
Rmd 7dd26b1 Xiang Zhu 2018-10-10 wflow_publish(“analysis/index.Rmd”)
html dd65113 Xiang Zhu 2018-09-21 Build site.
Rmd 283f43b Xiang Zhu 2018-09-21 wflow_publish(“analysis/index.Rmd”)
html f4e42f1 Xiang Zhu 2018-09-20 Build site.
Rmd 69cfef7 Xiang Zhu 2018-09-20 wflow_publish(“analysis/index.Rmd”)
html c08d574 Xiang Zhu 2018-09-19 Build site.
Rmd 3a196a1 Xiang Zhu 2018-09-19 wflow_publish(“analysis/index.Rmd”)
html b303bb7 Xiang Zhu 2018-09-04 Build site.
Rmd 665f7a3 Xiang Zhu 2018-09-04 wflow_publish(“analysis/index.Rmd”)
html 2a3e63f Xiang Zhu 2018-08-30 Build site.
Rmd a5d1757 Xiang Zhu 2018-08-30 wflow_publish(“analysis/index.Rmd”)
html 6142cc2 Xiang Zhu 2018-07-24 Build site.
Rmd d17ed5f Xiang Zhu 2018-07-24 wflow_publish(“analysis/index.Rmd”)
html b978776 Xiang Zhu 2018-07-24 Build site.
Rmd 1017c63 Xiang Zhu 2018-07-24 wflow_publish(“analysis/index.Rmd”)
html 9aaa70f Xiang Zhu 2018-07-20 Build site.
Rmd 2cd97ad Xiang Zhu 2018-07-20 wflow_publish(“analysis/index.Rmd”)
html 889612b Xiang Zhu 2018-07-19 Build site.
html fcdb217 Xiang Zhu 2018-07-19 Build site.
Rmd 041a3ef Xiang Zhu 2018-07-19 wflow_publish(files = c(“analysis/index.Rmd”, “analysis/license.Rmd”))
Rmd c07849b Xiang Zhu 2018-07-19 Start workflowr project.

Overview

This is my online notebook to document and share the full results of whole-genome integrated analyses of 38 gene regulatory networks and 18 human complex traits described in the following research article:

Zhu, X., Duren, Z. & Wong, W.H. Modeling regulatory network topology improves genome-wide analyses of complex human traits. Nat Commun 12, 2851 (2021). https://doi.org/10.1038/s41467-021-22588-0

If you find the analysis results, the pre-processed networks, the statistical methods, and/or the open-source software useful for your work, please kindly cite the research article listed above (Zhu et al, 2021).

If you have any question about the notebook and/or the article, please feel free to contact me xiangzhu[at]psu.edu.

Main results

For each phenotype below, please click to view network enrichment results, click to view gene prioritization results, and click to view gene cross-reference results. Please note that loading gene prioritization results may take a while because of the large number of genes displayed.

The network enrichment results () of each phenotype consist of RSS-NET enrichment Bayes factors of 38 inferred gene regulatory networks and 1 near-gene control network for the given trait, and enrichment \(P\)-values of LDSC and Pascal based on the same networks and GWAS data.

The gene prioritization results () of each phenotype consist of RSS-NET posterior probabilities of association (\(P_1\)) for all network genes under the baseline (\(M_0\)) and enrichment (\(M_1\)) models for the given trait.

The gene cross-reference results () of each phenotype consist of external information from Therapeutic Target Database (TTD), Mouse Genome Informatics (MGI) and Online Mendelian Inheritance in Man (OMIM).

Phenotype (GWAS publication) Network enrichment Gene prioritization Cross reference
Adult height (Wood et al. 2014) N/A
Body mass index (Locke et al. 2015)
Waist-to-hip ratio (Shungin et al. 2015)
Breast cancer (Michailidou et al. 2013)
Rheumatoid arthritis (Okada et al. 2014)
Crohn’s disease (Liu et al. 2015) N/A
Inflammatory bowel disease (Liu et al. 2015)
Ulcerative colitis (Liu et al. 2015)
High-density lipoprotein (Teslovich et al. 2010)
Low-density lipoprotein (Teslovich et al. 2010)
Type 2 diabetes (Morris et al. 2012)
Heart rate (den Hoed et al. 2013)
Coronary artery disease (Nikpay et al. 2015)
Myocardial infarction (Nikpay et al. 2015)
Atrial fibrillation (Christophersen et al. 2017)
Alzheimer’s disease (Lambert et al. 2013)
Schizophrenia (Ripke et al. 2014)
Neuroticism (Okbay et al. 2016)

Additional resources


Icons used in this notebook are credited to the Noun Project. This notebook is created using workflowr.


devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.1.0 (2021-05-18)
 os       Ubuntu 20.04.2 LTS          
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/New_York            
 date     2021-06-06                  

─ Packages ───────────────────────────────────────────────────────────────────
 package     * version date       lib source        
 bslib         0.2.5.1 2021-05-18 [3] CRAN (R 4.1.0)
 cachem        1.0.5   2021-05-15 [3] CRAN (R 4.0.5)
 callr         3.7.0   2021-04-20 [3] CRAN (R 4.0.5)
 cli           2.5.0   2021-04-26 [3] CRAN (R 4.0.5)
 crayon        1.4.1   2021-02-08 [3] CRAN (R 4.0.3)
 desc          1.3.0   2021-03-05 [3] CRAN (R 4.0.4)
 devtools      2.4.1   2021-05-05 [3] CRAN (R 4.0.5)
 digest        0.6.27  2020-10-24 [3] CRAN (R 4.0.3)
 ellipsis      0.3.2   2021-04-29 [3] CRAN (R 4.0.5)
 evaluate      0.14    2019-05-28 [3] CRAN (R 4.0.0)
 fansi         0.5.0   2021-05-25 [3] CRAN (R 4.1.0)
 fastmap       1.1.0   2021-01-25 [3] CRAN (R 4.0.3)
 fs            1.5.0   2020-07-31 [3] CRAN (R 4.0.2)
 git2r         0.28.0  2021-01-10 [1] CRAN (R 4.1.0)
 glue          1.4.2   2020-08-27 [3] CRAN (R 4.0.2)
 htmltools     0.5.1.1 2021-01-22 [3] CRAN (R 4.0.3)
 httpuv        1.6.1   2021-05-07 [3] CRAN (R 4.0.5)
 jquerylib     0.1.4   2021-04-26 [3] CRAN (R 4.0.5)
 jsonlite      1.7.2   2020-12-09 [3] CRAN (R 4.0.3)
 knitr         1.33    2021-04-24 [3] CRAN (R 4.0.5)
 later         1.2.0   2021-04-23 [3] CRAN (R 4.0.5)
 lifecycle     1.0.0   2021-02-15 [3] CRAN (R 4.0.4)
 magrittr      2.0.1   2020-11-17 [3] CRAN (R 4.0.3)
 memoise       2.0.0   2021-01-26 [3] CRAN (R 4.0.3)
 pillar        1.6.1   2021-05-16 [3] CRAN (R 4.0.5)
 pkgbuild      1.2.0   2020-12-15 [3] CRAN (R 4.0.3)
 pkgconfig     2.0.3   2019-09-22 [3] CRAN (R 4.0.0)
 pkgload       1.2.1   2021-04-06 [3] CRAN (R 4.0.5)
 prettyunits   1.1.1   2020-01-24 [3] CRAN (R 4.0.0)
 processx      3.5.2   2021-04-30 [3] CRAN (R 4.0.5)
 promises      1.2.0.1 2021-02-11 [3] CRAN (R 4.0.3)
 ps            1.6.0   2021-02-28 [3] CRAN (R 4.0.4)
 purrr         0.3.4   2020-04-17 [3] CRAN (R 4.0.0)
 R6            2.5.0   2020-10-28 [3] CRAN (R 4.0.3)
 Rcpp          1.0.6   2021-01-15 [3] CRAN (R 4.0.5)
 remotes       2.4.0   2021-06-02 [3] CRAN (R 4.1.0)
 rlang         0.4.11  2021-04-30 [3] CRAN (R 4.0.5)
 rmarkdown     2.8     2021-05-07 [3] CRAN (R 4.0.5)
 rprojroot     2.0.2   2020-11-15 [3] CRAN (R 4.0.3)
 sass          0.4.0   2021-05-12 [3] CRAN (R 4.0.5)
 sessioninfo   1.1.1   2018-11-05 [3] CRAN (R 4.0.0)
 stringi       1.6.2   2021-05-17 [3] CRAN (R 4.0.5)
 stringr       1.4.0   2019-02-10 [3] CRAN (R 4.0.0)
 testthat      3.0.2   2021-02-14 [3] CRAN (R 4.0.4)
 tibble        3.1.2   2021-05-16 [3] CRAN (R 4.0.5)
 usethis       2.0.1   2021-02-10 [3] CRAN (R 4.0.3)
 utf8          1.2.1   2021-03-12 [3] CRAN (R 4.0.4)
 vctrs         0.3.8   2021-04-29 [3] CRAN (R 4.0.5)
 whisker       0.4     2019-08-28 [3] CRAN (R 4.0.0)
 withr         2.4.2   2021-04-18 [3] CRAN (R 4.0.5)
 workflowr     1.6.2   2020-04-30 [1] CRAN (R 4.1.0)
 xfun          0.23    2021-05-15 [3] CRAN (R 4.0.5)
 yaml          2.2.1   2020-02-01 [3] CRAN (R 4.0.0)

[1] /home/maimaizhu/R/x86_64-pc-linux-gnu-library/4.1
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library