Enrichment results of low-density lipoprotein

Last updated: 2018-10-05

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File	Version	Author	Date	Message
html	1c85967	Xiang Zhu	2018-10-05	Build site.
html	e89fcbd	Xiang Zhu	2018-07-02	Build site.
Rmd	4ee8565	Xiang Zhu	2018-07-02	wflow_publish(“ldl_2010.Rmd”)

Input data

Results below were generated from the GWAS summary statistics published in the paper “Biological, Clinical and Population Relevance of 95 Loci for Blood Lipids” (Nature, 2010). The summary data file is available at http://csg.sph.umich.edu/willer/public/lipids2010.

Analysis results

Enrichment analyses are summarized by the following three quantities.

BF: Bayes factor comparing the enrichment model against the baseline model;
Outside \(\pi\): proportion of trait-associated SNPs that are “outside” the gene set;
Inside \(\pi\): proportion of trait-associated SNPs that are “inside” the gene set.

The first quantity reflects the significance of enrichment, whereas the last two capture the magnitude of enrichment. For each gene set, we report these three quantities in the last three columns of tables below, on log 10 scale.

Biological pathways

Tissue highly expressed genes

Tissue selectively expressed genes

Cluster distinctively expressed genes

The relationship between tissues and clusters is shown in Figure 1 of Dey et al. (2017); see below.

Session information

devtools::session_info()

Session info -------------------------------------------------------------

 setting  value                       
 version  R version 3.5.1 (2018-07-02)
 system   x86_64, darwin15.6.0        
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/Los_Angeles         
 date     2018-10-05

Packages -----------------------------------------------------------------

 package     * version date       source        
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 compiler      3.5.1   2018-07-05 local         
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 datasets    * 3.5.1   2018-07-05 local         
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 tools         3.5.1   2018-07-05 local         
 utils       * 3.5.1   2018-07-05 local         
 whisker       0.3-2   2013-04-28 CRAN (R 3.5.0)
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 xtable        1.8-3   2018-08-29 CRAN (R 3.5.0)
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