Last updated: 2018-09-03

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Input data

  • Processed GWAS file: /project/mstephens/test_rss/data/load2013/load2013_sumstat.mat
  • PECA2 liver-specific network: /scratch/PI/whwong/zduren/share/PECA_human/PECA2/Liver_network.txt
  • \(L_0\): 40 kb; \(L_1\): 100 kb
  • SNP-to-gene window: 10 Mb
  • SNP-to-RE window: exact zero
  • Hyperparameter grid: h=(0.05:0.05:0.75); piva=10.^(-(0.25:0.25:8))

Results summary

First look at the approximated log marginal likelihoods (elbo column below).

log10.piva sigb elbo time posp
-8.00 8.157307 1.851319e+18 137.01999 1
-8.00 7.880707 1.717878e+18 137.02130 0
-8.00 7.594040 1.513736e+18 119.69971 0
-8.00 7.296117 1.342198e+18 119.79866 0
-8.00 6.985500 2.469418e+17 119.69905 0
-7.50 3.745426 5.556589e+16 50.52394 0
-8.00 4.212415 1.167404e+16 67.85548 0
-7.75 4.178787 1.149902e+16 67.82137 0
-7.50 4.102908 9.131801e+15 67.77857 0
-8.00 3.648059 9.095235e+15 50.59115 0

Next look at the gene-level posterior statistics when the marginal likelihood is maximized.

hgnc_symbol chromosome_name start_position end_position gene_nid vb_weight vb_mean vb_var
OR11H1 22 16448824 16449805 17914 1 14725050758 66.5223548
POTEH 22 16256441 16287937 17913 1 5885504253 66.5409021
ARL17B 17 44352150 44439130 15107 1 3778441639 0.4774076
LRRC37A 17 44370099 44415160 15108 1 2912077495 0.8078529
STH 17 44076616 44077060 15105 1 2348272452 0.0911898
CBWD6 9 69204538 69269662 8588 1 953083761 66.5416603
FAM27A 9 45727107 45728274 8579 1 307269557 66.5416603
FOXD4L5 9 70175707 70178815 8590 1 237973730 66.5412604
FAM27E2 9 45733559 45734896 8580 1 168180809 66.5416603
FOXD4L6 9 69199480 69202204 8587 1 157571587 66.5416603

Session information

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] bindrcpp_0.2.2 DT_0.4         knitr_1.20     dplyr_0.7.5   
[5] R.matlab_3.6.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17      bindr_0.1.1       whisker_0.3-2    
 [4] magrittr_1.5      workflowr_1.1.1   tidyselect_0.2.4 
 [7] R6_2.2.2          rlang_0.2.1       highr_0.7        
[10] stringr_1.3.1     tools_3.5.1       R.oo_1.22.0      
[13] git2r_0.21.0      htmltools_0.3.6   yaml_2.1.19      
[16] rprojroot_1.3-2   digest_0.6.15     assertthat_0.2.0 
[19] tibble_1.4.2      purrr_0.2.5       htmlwidgets_1.2  
[22] R.utils_2.6.0     glue_1.2.0        evaluate_0.10.1  
[25] rmarkdown_1.10    stringi_1.2.3     pillar_1.2.3     
[28] compiler_3.5.1    backports_1.1.2   R.methodsS3_1.7.1
[31] pkgconfig_2.0.1

This reproducible R Markdown analysis was created with workflowr 1.1.1