Last updated: 2019-09-05

Checks: 7 0

Knit directory: rss-peca/

This reproducible R Markdown analysis was created with workflowr (version 1.4.0). 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 version displayed above was the version of the Git repository at the time these results were generated.

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/

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 R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
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 2018-09-20 Build site.
Rmd 3a196a1 Xiang Zhu 2018-09-20 wflow_publish(“analysis/index.Rmd”)
html b303bb7 Xiang Zhu 2018-09-05 Build site.
Rmd 665f7a3 Xiang Zhu 2018-09-05 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 regulatory networks and complex traits described in the manuscript:

TBA

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 our manuscript listed above, Zhu et al (2019).

If you have any question about the notebook and/or the manuscript, please feel free to contact me: Xiang Zhu, xiangzhu[at]stanford.edu.

Main results

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

Phenotype (GWAS publication) Network enrichment Gene prioritization
Adult height (Wood et al. 2014)
Rheumatoid arthritis (Okada et al. 2014)
Inflammatory bowel disease (Liu et al. 2015)
Low-density lipoprotein (Teslovich et al. 2010)
Coronary artery disease (Nikpay et al. 2015)
Atrial fibrillation (Christophersen et al. 2017)
Alzheimer’s disease (Lambert et al. 2013)
Schizophrenia (Ripke et al. 2014)

Additional resources

TBA


─ Session info ──────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.1 (2019-07-05)
 os       Ubuntu 18.04.3 LTS          
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/Los_Angeles         
 date     2019-09-05                  

─ Packages ──────────────────────────────────────────────────────────────
 package     * version date       lib source        
 assertthat    0.2.1   2019-03-21 [1] CRAN (R 3.6.0)
 backports     1.1.4   2019-04-10 [1] CRAN (R 3.6.0)
 callr         3.3.1   2019-07-18 [1] CRAN (R 3.6.1)
 cli           1.1.0   2019-03-19 [1] CRAN (R 3.6.0)
 crayon        1.3.4   2017-09-16 [1] CRAN (R 3.6.0)
 desc          1.2.0   2018-05-01 [1] CRAN (R 3.6.0)
 devtools      2.1.0   2019-07-06 [1] CRAN (R 3.6.1)
 digest        0.6.20  2019-07-04 [1] CRAN (R 3.6.1)
 evaluate      0.14    2019-05-28 [1] CRAN (R 3.6.0)
 fs            1.3.1   2019-05-06 [1] CRAN (R 3.6.0)
 git2r         0.26.1  2019-06-29 [1] CRAN (R 3.6.0)
 glue          1.3.1   2019-03-12 [1] CRAN (R 3.6.0)
 htmltools     0.3.6   2017-04-28 [1] CRAN (R 3.6.0)
 knitr         1.24    2019-08-08 [1] CRAN (R 3.6.1)
 magrittr      1.5     2014-11-22 [1] CRAN (R 3.6.0)
 memoise       1.1.0   2017-04-21 [1] CRAN (R 3.6.0)
 pkgbuild      1.0.5   2019-08-26 [1] CRAN (R 3.6.1)
 pkgload       1.0.2   2018-10-29 [1] CRAN (R 3.6.0)
 prettyunits   1.0.2   2015-07-13 [1] CRAN (R 3.6.0)
 processx      3.4.1   2019-07-18 [1] CRAN (R 3.6.1)
 ps            1.3.0   2018-12-21 [1] CRAN (R 3.6.0)
 R6            2.4.0   2019-02-14 [1] CRAN (R 3.6.0)
 Rcpp          1.0.2   2019-07-25 [1] CRAN (R 3.6.1)
 remotes       2.1.0   2019-06-24 [1] CRAN (R 3.6.0)
 rlang         0.4.0   2019-06-25 [1] CRAN (R 3.6.0)
 rmarkdown     1.15    2019-08-21 [1] CRAN (R 3.6.1)
 rprojroot     1.3-2   2018-01-03 [1] CRAN (R 3.6.0)
 sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 3.6.0)
 stringi       1.4.3   2019-03-12 [1] CRAN (R 3.6.0)
 stringr       1.4.0   2019-02-10 [1] CRAN (R 3.6.0)
 testthat      2.2.1   2019-07-25 [1] CRAN (R 3.6.1)
 usethis       1.5.1   2019-07-04 [1] CRAN (R 3.6.1)
 whisker       0.3-2   2013-04-28 [1] CRAN (R 3.6.0)
 withr         2.1.2   2018-03-15 [1] CRAN (R 3.6.0)
 workflowr     1.4.0   2019-06-08 [1] CRAN (R 3.6.0)
 xfun          0.9     2019-08-21 [1] CRAN (R 3.6.1)
 yaml          2.2.0   2018-07-25 [1] CRAN (R 3.6.0)

[1] /home/maimaizhu/R/x86_64-pc-linux-gnu-library/3.6
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library