Last updated: 2018-08-31

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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 windown: 10 Mb
  • Hyperparameter grid: TBA

Results summary

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

piva sigb elbo time
0.0001000 0.0515913 189566935.0 1047.9433
0.0001778 0.0386880 88426696.9 957.1887
0.0003162 0.0290119 64568073.4 1302.2966
0.0005623 0.0217559 35953379.4 1276.2622
0.0010000 0.0163146 16999449.9 1443.6655
0.0017783 0.0122342 6239008.6 1536.1694
0.0031623 0.0091744 1241460.2 1233.5987
0.1000000 0.0016315 -640022.0 4096.3463
0.3162278 0.0009174 -731651.6 3479.1000
0.1778279 0.0012234 -766687.1 3141.6219
0.5623413 0.0006880 -898377.8 2900.3702
0.0056234 0.0068798 -946876.3 3797.0045
0.0562341 0.0021756 -997159.9 3615.5936
0.0316228 0.0029012 -1100972.1 4003.9145
0.0100000 0.0051591 -1141247.3 4012.4360
0.0177828 0.0038688 -1435636.8 3133.8837

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
LGALS9B 17 20352708 20370852 14712 1 444.66672 0.0010826
OR11H1 22 16448824 16449805 17914 1 207.94006 0.0026617
CBWD6 9 69204538 69269662 8588 1 197.17232 0.0026617
RGL2 6 33259431 33267101 6194 1 167.12435 0.0005348
CDRT15L2 17 20483037 20484224 14713 1 162.23593 0.0006613
C16orf86 16 67700719 67702661 14191 1 132.58307 0.0000199
GALNT4 12 89913185 89920039 11797 1 128.69132 0.0000426
ARL17A 17 44594068 44657088 15110 1 93.25737 0.0004824
CLEC18B 16 74442529 74455368 14272 1 93.07069 0.0000250
ALOXE3 17 7999218 8022365 14590 1 74.02143 0.0000047

Look at top genes: LGALS9B, OR11H1, RGL2.

Session information

R version 3.5.0 (2018-04-23)
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_3.5.0       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_3.5.0    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