Last updated: 2022-02-13

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Rmd eb13ecf sq-96 2022-02-13 update
html e6bc169 sq-96 2022-02-13 Build site.
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Weight QC

[1] 11531

   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
1121  807  665  420  560  646  573  430  448  462  693  623  228  380  382  542 
  17   18   19   20   21   22 
 704  176  906  343  127  295 
[1] 8840
[1] 0.7666291

Load ctwas results

Check convergence of parameters


********************************************************
Note: As of version 1.0.0, cowplot does not change the
  default ggplot2 theme anymore. To recover the previous
  behavior, execute:
  theme_set(theme_cowplot())
********************************************************

Version Author Date
e6bc169 sq-96 2022-02-13
        gene          snp 
0.0114612037 0.0002790741 
    gene      snp 
17.33748 17.71301 
[1] 336107
[1]   11531 7535010
       gene         snp 
0.006817193 0.110820024 
[1]  0.08777756 17.62682168

Genes with highest PIPs

Version Author Date
e6bc169 sq-96 2022-02-13
           genename region_tag susie_pip        mu2          PVE         z
3434          CCND2       12_4 0.9754463   28.48023 8.265505e-05 -5.119990
983          PIK3C3      18_23 0.9391838   51.83807 1.448511e-04  6.828125
8986        C1QTNF4      11_29 0.9283841 1287.45131 3.556157e-03 11.152141
507           KCNH2       7_93 0.9260291   43.03560 1.185700e-04  6.514694
4444          TRAF3      14_54 0.9110077   60.27067 1.633618e-04 -8.170458
12533          ETV5      3_114 0.9061125   94.53246 2.548505e-04  9.862284
5033          DCAF7      17_37 0.9006528   28.31246 7.586780e-05  5.436897
1797       PPP1R16B      20_23 0.9001065   21.05218 5.637849e-05 -4.128732
8020          CASP7      10_71 0.8958497   24.19811 6.449693e-05  4.584307
9598         ZBTB41       1_98 0.8825101 1744.48636 4.580466e-03  4.618133
6041           ECE2      3_113 0.8423885   29.53188 7.401607e-05 -5.315245
13701  RP11-823E8.3      12_54 0.7583472  102.47935 2.312208e-04 -6.438012
10915       ZKSCAN5       7_61 0.7329540   52.16379 1.137544e-04  7.133466
7609       SERPINI1      3_103 0.7283402   21.22901 4.600304e-05 -4.173167
3223          EDEM3       1_92 0.7278036   28.49638 6.170584e-05  5.237828
13885      PRICKLE4       6_32 0.7231084   23.68968 5.096653e-05 -4.797384
12931 RP11-218E20.3      14_20 0.7194148   21.31974 4.563349e-05 -3.497273
13700         NOL12      22_15 0.7136705   28.47621 6.046477e-05 -4.158975
6995         DYRK1A      21_18 0.7102180   21.11569 4.461895e-05 -4.005566
11862         TEX40      11_36 0.7099352   30.73452 6.491837e-05 -5.495304
      num_eqtl
3434         1
983          2
8986         2
507          2
4444         1
12533        1
5033         1
1797         1
8020         1
9598         1
6041         1
13701        1
10915        1
7609         2
3223         1
13885        1
12931        2
13700        1
6995         1
11862        1

Genes with largest effect sizes

Version Author Date
e6bc169 sq-96 2022-02-13
          genename region_tag    susie_pip      mu2          PVE         z
135           NADK        1_1 0.000000e+00 34222.51 0.000000e+00  4.858945
9678         STX19       3_59 0.000000e+00 31351.20 0.000000e+00 -5.059656
10427         GSAP       7_49 3.330669e-16 31261.52 3.097876e-17  5.259703
2201        PIK3R2      19_14 0.000000e+00 28046.82 0.000000e+00  5.620989
12651 CTD-3074O7.2      11_37 6.960668e-08 26961.48 5.583637e-09 -4.560522
12665 RP11-757G1.6      11_38 2.703764e-01 24015.26 1.931873e-02  4.314321
5499         MFAP1      15_16 0.000000e+00 23943.73 0.000000e+00  4.302998
11029       MRPL21      11_38 1.278463e-03 23927.47 9.101383e-05  4.378813
4902          HEY2       6_84 0.000000e+00 23615.44 0.000000e+00  3.066031
756          MAPK6      15_21 7.397585e-03 23518.62 5.176359e-04 -4.661687
8147          LEO1      15_21 5.342720e-04 23367.26 3.714435e-05  4.647326
13664    LINC02019       3_35 1.111514e-07 22718.56 7.513084e-09 -4.361776
4212         TMOD2      15_21 0.000000e+00 22290.10 0.000000e+00  4.402599
5505        LYSMD2      15_21 0.000000e+00 22290.10 0.000000e+00  4.402599
1379         WDR76      15_16 0.000000e+00 21870.59 0.000000e+00  4.420440
11904       CKMT1A      15_16 0.000000e+00 21444.58 0.000000e+00  4.129652
3034          CISH       3_35 0.000000e+00 20421.81 0.000000e+00 -3.798838
10708         DPYD       1_60 0.000000e+00 19375.41 0.000000e+00 -2.963185
3033         HEMK1       3_35 0.000000e+00 19267.38 0.000000e+00 -4.681781
13533    U91328.19       6_20 0.000000e+00 18946.90 0.000000e+00 -5.327444
      num_eqtl
135          2
9678         1
10427        1
2201         1
12651        2
12665        2
5499         1
11029        1
4902         1
756          1
8147         1
13664        2
4212         1
5505         1
1379         2
11904        1
3034         1
10708        2
3033         1
13533        2

Genes with highest PVE

          genename region_tag   susie_pip         mu2          PVE          z
12665 RP11-757G1.6      11_38 0.270376414 24015.26131 0.0193187296   4.314321
6352         CELF1      11_29 0.300032757 13975.32342 0.0124753570  -3.558425
2658        PTPMT1      11_29 0.300032757 13975.32342 0.0124753570  -3.558425
276           CPS1      2_124 0.529442940  4711.26810 0.0074212903  -3.534889
6638         PANK1      10_57 0.320040553  6099.69658 0.0058081214  -3.857131
9598        ZBTB41       1_98 0.882510094  1744.48636 0.0045804664   4.618133
8986       C1QTNF4      11_29 0.928384135  1287.45131 0.0035561573  11.152141
756          MAPK6      15_21 0.007397585 23518.62488 0.0005176359  -4.661687
10898        AFAP1        4_9 0.244593919   587.89707 0.0004278282   4.141770
12533         ETV5      3_114 0.906112531    94.53246 0.0002548505   9.862284
11901        VPS52       6_28 0.677229488   124.40308 0.0002506625   1.606101
11712       NDUFS3      11_29 0.059984100  1353.71774 0.0002415943 -10.873568
13701 RP11-823E8.3      12_54 0.758347226   102.47935 0.0002312208  -6.438012
4444         TRAF3      14_54 0.911007692    60.27067 0.0001633618  -8.170458
983         PIK3C3      18_23 0.939183786    51.83807 0.0001448511   6.828125
507          KCNH2       7_93 0.926029131    43.03560 0.0001185700   6.514694
9411         NUPR1      16_23 0.606521428    63.67678 0.0001149078 -10.467590
10915      ZKSCAN5       7_61 0.732954014    52.16379 0.0001137544   7.133466
5638       C18orf8      18_12 0.596520583    56.75826 0.0001007342   7.506065
13896       DHRS11      17_22 0.545530664    61.61665 0.0001000091  -8.128326
      num_eqtl
12665        2
6352         1
2658         1
276          1
6638         1
9598         1
8986         2
756          1
10898        2
12533        1
11901        1
11712        1
13701        1
4444         1
983          2
507          2
9411         2
10915        1
5638         2
13896        1

Genes with largest z scores

      genename region_tag    susie_pip        mu2          PVE          z
34        RBM6       3_35 1.402477e-03  914.63290 3.816498e-06  12.536042
9289    KCTD13      16_24 1.257730e-01  109.37426 4.092843e-05 -11.490673
7735     MST1R       3_35 1.837709e-10  233.55147 1.276973e-13 -11.458475
8986   C1QTNF4      11_29 9.283841e-01 1287.45131 3.556157e-03  11.152141
7729    RNF123       3_35 1.685874e-11  829.59627 4.161159e-14 -10.957103
1860     MAPK3      16_24 2.535695e-02   97.55336 7.359726e-06  10.880016
11712   NDUFS3      11_29 5.998410e-02 1353.71774 2.415943e-04 -10.873568
9411     NUPR1      16_23 6.065214e-01   63.67678 1.149078e-04 -10.467590
12230   NPIPB7      16_23 5.870822e-02   62.11709 1.085007e-05  10.428973
8623    INO80E      16_24 4.238999e-02   86.80742 1.094820e-05  10.393266
10945 C6orf106       6_28 4.877039e-05  118.65415 1.721716e-08 -10.263559
640   UHRF1BP1       6_28 1.556172e-05   97.68565 4.522835e-09  10.203329
12533     ETV5      3_114 9.061125e-01   94.53246 2.548505e-04   9.862284
1952     BCKDK      16_24 1.729060e-02   67.72884 3.484224e-06  -9.555938
7733     CAMKV       3_35 0.000000e+00 1461.85648 0.000000e+00  -9.545115
2608     MTCH2      11_29 3.574918e-14  508.57667 5.409349e-17  -9.514152
10920  FAM180B      11_29 1.743050e-14  504.81784 2.617984e-17  -9.432202
1953      KAT8      16_24 1.835660e-02   63.59798 3.473425e-06  -9.181240
8987     NEGR1       1_46 6.022882e-01   44.67110 8.004855e-05  -8.928461
10248    APOBR      16_23 9.617590e-03   41.37761 1.184006e-06  -8.734610
      num_eqtl
34           1
9289         1
7735         2
8986         2
7729         1
1860         1
11712        1
9411         2
12230        1
8623         2
10945        1
640          2
12533        1
1952         2
7733         2
2608         1
10920        1
1953         2
8987         1
10248        1

Comparing z scores and PIPs

Version Author Date
e6bc169 sq-96 2022-02-13

Version Author Date
e6bc169 sq-96 2022-02-13
[1] 0.02350186
      genename region_tag    susie_pip        mu2          PVE          z
34        RBM6       3_35 1.402477e-03  914.63290 3.816498e-06  12.536042
9289    KCTD13      16_24 1.257730e-01  109.37426 4.092843e-05 -11.490673
7735     MST1R       3_35 1.837709e-10  233.55147 1.276973e-13 -11.458475
8986   C1QTNF4      11_29 9.283841e-01 1287.45131 3.556157e-03  11.152141
7729    RNF123       3_35 1.685874e-11  829.59627 4.161159e-14 -10.957103
1860     MAPK3      16_24 2.535695e-02   97.55336 7.359726e-06  10.880016
11712   NDUFS3      11_29 5.998410e-02 1353.71774 2.415943e-04 -10.873568
9411     NUPR1      16_23 6.065214e-01   63.67678 1.149078e-04 -10.467590
12230   NPIPB7      16_23 5.870822e-02   62.11709 1.085007e-05  10.428973
8623    INO80E      16_24 4.238999e-02   86.80742 1.094820e-05  10.393266
10945 C6orf106       6_28 4.877039e-05  118.65415 1.721716e-08 -10.263559
640   UHRF1BP1       6_28 1.556172e-05   97.68565 4.522835e-09  10.203329
12533     ETV5      3_114 9.061125e-01   94.53246 2.548505e-04   9.862284
1952     BCKDK      16_24 1.729060e-02   67.72884 3.484224e-06  -9.555938
7733     CAMKV       3_35 0.000000e+00 1461.85648 0.000000e+00  -9.545115
2608     MTCH2      11_29 3.574918e-14  508.57667 5.409349e-17  -9.514152
10920  FAM180B      11_29 1.743050e-14  504.81784 2.617984e-17  -9.432202
1953      KAT8      16_24 1.835660e-02   63.59798 3.473425e-06  -9.181240
8987     NEGR1       1_46 6.022882e-01   44.67110 8.004855e-05  -8.928461
10248    APOBR      16_23 9.617590e-03   41.37761 1.184006e-06  -8.734610
      num_eqtl
34           1
9289         1
7735         2
8986         2
7729         1
1860         1
11712        1
9411         2
12230        1
8623         2
10945        1
640          2
12533        1
1952         2
7733         2
2608         1
10920        1
1953         2
8987         1
10248        1

Sensitivity, specificity and precision for silver standard genes

[1] 41
[1] 25
[1] 4.594584
[1] 11
[1] 271
     genename region_tag susie_pip      mu2          PVE         z num_eqtl
8020    CASP7      10_71 0.8958497 24.19811 6.449693e-05  4.584307        1
1797 PPP1R16B      20_23 0.9001065 21.05218 5.637849e-05 -4.128732        1
    ctwas      TWAS 
0.0000000 0.1219512 
    ctwas      TWAS 
0.9990440 0.9768816 
     ctwas       TWAS 
0.00000000 0.01845018 

Version Author Date
e6bc169 sq-96 2022-02-13

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] readxl_1.3.1    cowplot_1.0.0   ggplot2_3.3.5   workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.1  xfun_0.29         purrr_0.3.4       colorspace_2.0-2 
 [5] vctrs_0.3.8       generics_0.1.1    htmltools_0.5.2   yaml_2.2.1       
 [9] utf8_1.2.2        blob_1.2.2        rlang_0.4.12      jquerylib_0.1.4  
[13] later_0.8.0       pillar_1.6.4      glue_1.5.1        withr_2.4.3      
[17] DBI_1.1.1         bit64_4.0.5       lifecycle_1.0.1   stringr_1.4.0    
[21] cellranger_1.1.0  munsell_0.5.0     gtable_0.3.0      evaluate_0.14    
[25] memoise_2.0.1     labeling_0.4.2    knitr_1.36        fastmap_1.1.0    
[29] httpuv_1.5.1      fansi_0.5.0       highr_0.9         Rcpp_1.0.7       
[33] promises_1.0.1    scales_1.1.1      cachem_1.0.6      farver_2.1.0     
[37] fs_1.5.2          bit_4.0.4         digest_0.6.29     stringi_1.7.6    
[41] dplyr_1.0.7       rprojroot_2.0.2   grid_3.6.1        tools_3.6.1      
[45] magrittr_2.0.1    tibble_3.1.6      RSQLite_2.2.8     crayon_1.4.2     
[49] whisker_0.3-2     pkgconfig_2.0.3   ellipsis_0.3.2    data.table_1.14.2
[53] assertthat_0.2.1  rmarkdown_2.11    R6_2.5.1          git2r_0.26.1     
[57] compiler_3.6.1