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] 10973

   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
1076  769  643  427  529  614  510  402  415  437  663  585  220  377  370  516 
  17   18   19   20   21   22 
 664  166  865  330  117  278 
[1] 8798
[1] 0.8017862

Load ctwas results

Check convergence of parameters


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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())
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Version Author Date
e6bc169 sq-96 2022-02-13
        gene          snp 
0.0074990118 0.0002925305 
    gene      snp 
23.53208 17.52845 
[1] 336107
[1]   10973 7535010
       gene         snp 
0.005761189 0.114953178 
[1]  0.2223438 18.6718962

Genes with highest PIPs

Version Author Date
e6bc169 sq-96 2022-02-13
       genename region_tag susie_pip         mu2          PVE          z
717       MAPK6      15_21 1.0000000 34111.65582 1.014905e-01  -4.600218
10029      GSAP       7_49 1.0000000 32344.91724 9.623399e-02   5.259703
7429      PPM1M       3_36 1.0000000   241.22300 7.176970e-04   4.468299
9989     ARL17A      17_27 0.9436863    32.40929 9.099544e-05   5.324914
1199     DYNLL1      12_74 0.9379920    59.07720 1.648699e-04  -5.805664
12053      ETV5      3_114 0.9122369    96.75415 2.626030e-04   9.862284
8671     EFEMP2      11_36 0.7914194    56.03230 1.319373e-04  -8.200649
3564      ZMIZ2       7_33 0.7782787    66.49342 1.539700e-04  -8.105339
9621      KCNB2       8_53 0.7522135    66.18833 1.481307e-04  -8.225507
13243 HIST1H2BE       6_20 0.7440818    31.09955 6.884892e-05  -6.515410
5796       ECE2      3_113 0.7149013    29.87117 6.353613e-05  -5.305115
1445      DERL3       22_6 0.6864450    22.98366 4.694047e-05   4.036538
7736    R3HCC1L      10_62 0.6829995    40.51919 8.233861e-05   7.438889
13421  PRICKLE4       6_32 0.6622145    24.65458 4.857567e-05  -4.797384
8923     ASPHD1      16_24 0.6555724   578.63592 1.128622e-03 -11.937656
11969    ATP5J2       7_61 0.6481907    53.45298 1.030854e-04  -7.116991
10750     UCKL1      20_38 0.6400369    25.30589 4.818913e-05   3.572515
151       CSDE1       1_71 0.6372136    22.68257 4.300311e-05  -4.744544
6243     DPYSL4      10_83 0.6345369    43.78509 8.266194e-05  -6.800654
9938     GPRIN3       4_60 0.6310406    25.08359 4.709442e-05  -3.768703
      num_eqtl
717          1
10029        1
7429         2
9989         1
1199         1
12053        1
8671         1
3564         1
9621         1
13243        1
5796         1
1445         1
7736         1
13421        1
8923         1
11969        1
10750        1
151          1
6243         1
9938         2

Genes with largest effect sizes

Version Author Date
e6bc169 sq-96 2022-02-13
      genename region_tag    susie_pip      mu2          PVE          z
10      SEMA3F       3_35 0.000000e+00 73861.11 0.000000e+00   7.681163
10261  SLC38A3       3_35 0.000000e+00 69033.76 0.000000e+00   6.725828
7591   CCDC171       9_13 0.000000e+00 44932.09 0.000000e+00   7.405453
8624     NEGR1       1_46 0.000000e+00 43597.35 0.000000e+00 -10.374619
40        RBM6       3_35 0.000000e+00 41746.10 0.000000e+00  12.536042
6640    ZNF689      16_24 0.000000e+00 39994.39 0.000000e+00  -6.014416
7425     MST1R       3_35 0.000000e+00 35623.61 0.000000e+00 -12.634816
717      MAPK6      15_21 1.000000e+00 34111.66 1.014905e-01  -4.600218
10029     GSAP       7_49 1.000000e+00 32344.92 9.623399e-02   5.259703
9293     STX19       3_59 0.000000e+00 31600.11 0.000000e+00  -5.059656
9289     DHFR2       3_59 0.000000e+00 25976.41 0.000000e+00   4.031467
5274     MFAP1      15_16 1.202121e-06 24146.55 8.636263e-08   4.302998
7420    RNF123       3_35 0.000000e+00 23601.01 0.000000e+00 -10.959165
12024     NAT6       3_35 0.000000e+00 23005.37 0.000000e+00  -6.362236
10512 C6orf106       6_29 0.000000e+00 22878.38 0.000000e+00   2.961936
11433   CKMT1A      15_16 0.000000e+00 21624.66 0.000000e+00   4.129652
1326     WDR76      15_16 0.000000e+00 21190.22 0.000000e+00   4.963393
1785    ZNF629      16_24 0.000000e+00 20375.42 0.000000e+00   4.335360
10290     DPYD       1_60 0.000000e+00 19960.73 0.000000e+00  -3.213351
10101    HYAL3       3_35 0.000000e+00 18111.05 0.000000e+00   6.242668
      num_eqtl
10           1
10261        1
7591         2
8624         2
40           1
6640         1
7425         2
717          1
10029        1
9293         1
9289         2
5274         1
7420         1
12024        1
10512        1
11433        1
1326         2
1785         1
10290        1
10101        2

Genes with highest PVE

      genename region_tag  susie_pip         mu2          PVE          z
717      MAPK6      15_21 1.00000000 34111.65582 1.014905e-01  -4.600218
10029     GSAP       7_49 1.00000000 32344.91724 9.623399e-02   5.259703
821       SDHA        5_1 0.22996475 12142.57236 8.307960e-03   2.906571
8923    ASPHD1      16_24 0.65557239   578.63592 1.128622e-03 -11.937656
7429     PPM1M       3_36 0.99999995   241.22300 7.176970e-04   4.468299
12053     ETV5      3_114 0.91223693    96.75415 2.626030e-04   9.862284
6834     ADPGK      15_34 0.05906579  1201.54605 2.111538e-04   5.872014
1199    DYNLL1      12_74 0.93799195    59.07720 1.648699e-04  -5.805664
3564     ZMIZ2       7_33 0.77827868    66.49342 1.539700e-04  -8.105339
9621     KCNB2       8_53 0.75221351    66.18833 1.481307e-04  -8.225507
6587     GPR61       1_67 0.58712009    79.87169 1.395219e-04   8.755235
5143      USO1       4_51 0.37686900   123.86534 1.388873e-04  -2.133639
8671    EFEMP2      11_36 0.79141941    56.03230 1.319373e-04  -8.200649
9035     NUPR1      16_23 0.55508807    69.66893 1.150598e-04 -10.643364
11969   ATP5J2       7_61 0.64819070    53.45298 1.030854e-04  -7.116991
10366 SLC35E2B        1_1 0.50528267    63.52597 9.550105e-05  -7.654473
12120   CDK11B        1_1 0.50528267    63.52597 9.550105e-05  -7.654473
9989    ARL17A      17_27 0.94368626    32.40929 9.099544e-05   5.324914
6243    DPYSL4      10_83 0.63453692    43.78509 8.266194e-05  -6.800654
7736   R3HCC1L      10_62 0.68299949    40.51919 8.233861e-05   7.438889
      num_eqtl
717          1
10029        1
821          1
8923         1
7429         2
12053        1
6834         3
1199         1
3564         1
9621         1
6587         1
5143         1
8671         1
9035         2
11969        1
10366        1
12120        1
9989         1
6243         1
7736         1

Genes with largest z scores

           genename region_tag    susie_pip         mu2          PVE          z
7425          MST1R       3_35 0.000000e+00 35623.60624 0.000000e+00 -12.634816
40             RBM6       3_35 0.000000e+00 41746.09899 0.000000e+00  12.536042
8923         ASPHD1      16_24 6.555724e-01   578.63592 1.128622e-03 -11.937656
8924         KCTD13      16_24 4.363856e-03   498.26763 6.469273e-06  11.490673
8275         INO80E      16_24 1.638102e-04  1631.74862 7.952738e-07  11.076716
7420         RNF123       3_35 0.000000e+00 23601.01392 0.000000e+00 -10.959165
6146          TAOK2      16_24 4.676057e-06  1891.49051 2.631518e-08  10.737701
9035          NUPR1      16_23 5.550881e-01    69.66893 1.150598e-04 -10.643364
8624          NEGR1       1_46 0.000000e+00 43597.35168 0.000000e+00 -10.374619
11727 RP11-196G11.6      16_24 4.163481e-08  7371.38703 9.131207e-10  10.011241
8623        C1QTNF4      11_29 2.296909e-02    95.37723 6.517949e-06   9.951168
12053          ETV5      3_114 9.122369e-01    96.75415 2.626030e-04   9.862284
5469           SAE1      19_33 4.553008e-03   100.30006 1.358695e-06   9.848747
461           PRSS8      16_24 2.774712e-09  6922.86884 5.715134e-11  -9.764760
7720          RAPSN      11_29 1.189135e-02    88.20982 3.120834e-06   9.728710
11241           LAT      16_23 2.439066e-01    56.17058 4.076195e-05  -9.552834
2491          MTCH2      11_29 9.481212e-03    83.09943 2.344144e-06  -9.514152
10579          IL27      16_23 6.175921e-03    50.93657 9.359526e-07   9.140265
3527           POLK       5_44 1.241711e-02    53.54319 1.978094e-06   8.883506
7718       SLC39A13      11_29 9.707601e-03    72.48101 2.093431e-06  -8.831101
      num_eqtl
7425         2
40           1
8923         1
8924         1
8275         1
7420         1
6146         1
9035         2
8624         2
11727        1
8623         2
12053        1
5469         1
461          1
7720         1
11241        1
2491         1
10579        1
3527         1
7718         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] 0.02159847
           genename region_tag    susie_pip         mu2          PVE          z
7425          MST1R       3_35 0.000000e+00 35623.60624 0.000000e+00 -12.634816
40             RBM6       3_35 0.000000e+00 41746.09899 0.000000e+00  12.536042
8923         ASPHD1      16_24 6.555724e-01   578.63592 1.128622e-03 -11.937656
8924         KCTD13      16_24 4.363856e-03   498.26763 6.469273e-06  11.490673
8275         INO80E      16_24 1.638102e-04  1631.74862 7.952738e-07  11.076716
7420         RNF123       3_35 0.000000e+00 23601.01392 0.000000e+00 -10.959165
6146          TAOK2      16_24 4.676057e-06  1891.49051 2.631518e-08  10.737701
9035          NUPR1      16_23 5.550881e-01    69.66893 1.150598e-04 -10.643364
8624          NEGR1       1_46 0.000000e+00 43597.35168 0.000000e+00 -10.374619
11727 RP11-196G11.6      16_24 4.163481e-08  7371.38703 9.131207e-10  10.011241
8623        C1QTNF4      11_29 2.296909e-02    95.37723 6.517949e-06   9.951168
12053          ETV5      3_114 9.122369e-01    96.75415 2.626030e-04   9.862284
5469           SAE1      19_33 4.553008e-03   100.30006 1.358695e-06   9.848747
461           PRSS8      16_24 2.774712e-09  6922.86884 5.715134e-11  -9.764760
7720          RAPSN      11_29 1.189135e-02    88.20982 3.120834e-06   9.728710
11241           LAT      16_23 2.439066e-01    56.17058 4.076195e-05  -9.552834
2491          MTCH2      11_29 9.481212e-03    83.09943 2.344144e-06  -9.514152
10579          IL27      16_23 6.175921e-03    50.93657 9.359526e-07   9.140265
3527           POLK       5_44 1.241711e-02    53.54319 1.978094e-06   8.883506
7718       SLC39A13      11_29 9.707601e-03    72.48101 2.093431e-06  -8.831101
      num_eqtl
7425         2
40           1
8923         1
8924         1
8275         1
7420         1
6146         1
9035         2
8624         2
11727        1
8623         2
12053        1
5469         1
461          1
7720         1
11241        1
2491         1
10579        1
3527         1
7718         1

Sensitivity, specificity and precision for silver standard genes

[1] 41
[1] 25
[1] 4.584229
[1] 6
[1] 237
     genename region_tag susie_pip     mu2         PVE        z num_eqtl
7429    PPM1M       3_36         1 241.223 0.000717697 4.468299        2
     ctwas       TWAS 
0.00000000 0.09756098 
    ctwas      TWAS 
0.9994520 0.9787176 
     ctwas       TWAS 
0.00000000 0.01687764 

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