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.
Rmd 87fee8b sq-96 2022-02-13 update

Introduction

Weight QC

[1] 10532

   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
1032  741  611  415  500  593  513  394  399  413  617  585  228  354  366  467 
  17   18   19   20   21   22 
 630  170  801  314  124  265 
[1] 8584
[1] 0.8150399

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 
0.0053427438 0.0002972845 
    gene      snp 
30.33477 17.09673 
[1] 336107
[1]   10532 7535010
       gene         snp 
0.005078533 0.113944037 
[1]  0.4380626 15.3065312

Genes with highest PIPs

Version Author Date
e6bc169 sq-96 2022-02-13
           genename region_tag susie_pip         mu2          PVE         z
9777        KLHDC8B       3_34 1.0000000  2542.57627 7.564782e-03 -5.051557
789            SDHA        5_1 1.0000000 21042.52138 6.260661e-02  3.012479
11293    AC078842.3       7_84 1.0000000 19171.29914 5.703927e-02 -3.207993
4274        IGHMBP2      11_38 1.0000000 31336.96431 9.323508e-02 -4.378813
5140          MFAP1      15_16 1.0000000 29203.27973 8.688685e-02  4.302998
695           MAPK6      15_21 1.0000000 28649.03417 8.523784e-02 -4.646216
7232          PPM1M       3_36 0.9999999   352.45212 1.048631e-03  4.731816
1472          ASCC2      22_10 0.7776235  8574.76169 1.983873e-02 -2.815534
8471         EFEMP2      11_36 0.7758290    50.60634 1.168136e-04 -7.483691
12868         PANO1       11_1 0.7575940    27.27802 6.148538e-05  4.978592
3443          ZMIZ2       7_33 0.7504608    67.76347 1.513025e-04 -8.105339
7328          ZNF12        7_9 0.7474493    28.09975 6.248944e-05  5.064700
1464          RASD2      22_14 0.7402740    24.87497 5.478700e-05 -4.361708
12828 RP11-340F14.6      12_74 0.7297061    30.01736 6.516929e-05 -4.742464
11162         VPS52       6_28 0.7203038   127.03285 2.722414e-04  1.606101
2760         PDCD10      3_103 0.7017297    23.84490 4.978378e-05 -4.064505
2845          ITGB6       2_96 0.6533228    59.14060 1.149572e-04  5.514945
3959          KLK14      19_35 0.6372520    28.25002 5.356147e-05 -4.061766
1588           NINL      20_19 0.6092758    34.74160 6.297761e-05 -5.532192
1304           CBX5      12_33 0.6017194    25.83998 4.626033e-05  4.691159
      num_eqtl
9777         2
789          1
11293        1
4274         1
5140         1
695          1
7232         2
1472         2
8471         2
12868        2
3443         1
7328         2
1464         2
12828        2
11162        1
2760         1
2845         1
3959         1
1588         2
1304         1

Genes with largest effect sizes

Version Author Date
e6bc169 sq-96 2022-02-13
        genename region_tag susie_pip      mu2        PVE          z num_eqtl
10032    SLC38A3       3_35         0 66888.53 0.00000000   6.725828        1
7397     CCDC171       9_13         0 42632.91 0.00000000   8.471161        2
38          RBM6       3_35         0 40475.73 0.00000000  12.536042        1
7227       MST1R       3_35         0 34543.29 0.00000000 -12.635394        2
8111      CALML6        1_1         0 32850.88 0.00000000  -5.718338        1
4274     IGHMBP2      11_38         1 31336.96 0.09323508  -4.378813        1
9078       STX19       3_59         0 30618.53 0.00000000  -5.059656        1
5140       MFAP1      15_16         1 29203.28 0.08688685   4.302998        1
695        MAPK6      15_21         1 28649.03 0.08523784  -4.646216        1
1280       WDR76      15_16         0 25920.29 0.00000000   4.454356        1
2418       CPT1A      11_38         0 24846.46 0.00000000  -4.676837        1
4970       TMOD3      15_21         0 23045.27 0.00000000   5.411998        1
7223      RNF123       3_35         0 22889.67 0.00000000 -10.959165        1
789         SDHA        5_1         1 21042.52 0.06260661   3.012479        1
4873     TUBGCP4      15_16         0 20509.43 0.00000000   3.366163        1
11293 AC078842.3       7_84         1 19171.30 0.05703927  -3.207993        1
7966        ADAL      15_16         0 17919.16 0.00000000  -2.861302        1
7967       LCMT2      15_16         0 17919.16 0.00000000  -2.861302        1
9868       HYAL3       3_35         0 17850.05 0.00000000   6.264073        2
859         MCM6       2_80         0 17636.26 0.00000000  -3.886179        1

Genes with highest PVE

           genename region_tag  susie_pip         mu2          PVE          z
4274        IGHMBP2      11_38 1.00000000 31336.96431 9.323508e-02  -4.378813
5140          MFAP1      15_16 1.00000000 29203.27973 8.688685e-02   4.302998
695           MAPK6      15_21 1.00000000 28649.03417 8.523784e-02  -4.646216
789            SDHA        5_1 1.00000000 21042.52138 6.260661e-02   3.012479
11293    AC078842.3       7_84 1.00000000 19171.29914 5.703927e-02  -3.207993
1472          ASCC2      22_10 0.77762350  8574.76169 1.983873e-02  -2.815534
9777        KLHDC8B       3_34 1.00000000  2542.57627 7.564782e-03  -5.051557
262            CPS1      2_124 0.49202420  4722.14667 6.912711e-03   3.534889
2872         LANCL1      2_124 0.49202420  4722.14667 6.912711e-03  -3.534889
7232          PPM1M       3_36 0.99999991   352.45212 1.048631e-03   4.731816
11162         VPS52       6_28 0.72030380   127.03285 2.722414e-04   1.606101
8727         ASPHD1      16_24 0.59150663   120.67330 2.123700e-04 -11.848514
10189        ATP2A1      16_23 0.50557684   100.96198 1.518684e-04 -10.759014
3443          ZMIZ2       7_33 0.75046079    67.76347 1.513025e-04  -8.105339
6433          GPR61       1_67 0.56829014    81.16210 1.372290e-04   8.755235
10756        LY6G5C       6_26 0.43404866   106.00275 1.368920e-04   8.417860
12619 CTD-2186M15.3       5_22 0.02120586  2014.86154 1.271228e-04   2.933876
8471         EFEMP2      11_36 0.77582899    50.60634 1.168136e-04  -7.483691
2845          ITGB6       2_96 0.65332282    59.14060 1.149572e-04   5.514945
13013        DHRS11      17_22 0.51954196    63.45942 9.809326e-05  -8.128326
      num_eqtl
4274         1
5140         1
695          1
789          1
11293        1
1472         2
9777         2
262          1
2872         1
7232         2
11162        1
8727         1
10189        1
3443         1
6433         1
10756        1
12619        2
8471         2
2845         1
13013        1

Genes with largest z scores

       genename region_tag    susie_pip         mu2          PVE          z
7227      MST1R       3_35 0.000000e+00 34543.28743 0.000000e+00 -12.635394
38         RBM6       3_35 0.000000e+00 40475.72984 0.000000e+00  12.536042
8727     ASPHD1      16_24 5.915066e-01   120.67330 2.123700e-04 -11.848514
1048      EFR3B       2_15 1.114961e-08   203.24843 6.742318e-12  11.586593
8728     KCTD13      16_24 6.773020e-02   115.83721 2.334280e-05 -11.490673
8068     INO80E      16_24 1.260053e-02   103.17532 3.868004e-06  11.076716
7223     RNF123       3_35 0.000000e+00 22889.67075 0.000000e+00 -10.959165
1721      MAPK3      16_24 1.145581e-02   103.03163 3.511713e-06  10.880016
10189    ATP2A1      16_23 5.055768e-01   100.96198 1.518684e-04 -10.759014
11438    NPIPB7      16_23 7.272766e-02   100.96337 2.184670e-05  10.509650
10225   SULT1A1      16_23 2.946593e-02    99.06621 8.684967e-06  10.367233
10271  C6orf106       6_28 5.814351e-05   124.59696 2.155416e-08 -10.263559
10322   SULT1A2      16_23 1.683314e-02    95.71737 4.793783e-06 -10.171155
7747     ZNF668      16_24 1.090314e-01    80.22421 2.602433e-05  10.000364
5341       SAE1      19_33 1.095253e-03   100.68705 3.281034e-07   9.848747
8426    C1QTNF4      11_29 6.345703e-03    90.11964 1.701460e-06   9.563515
11752 LINC00461       5_52 8.338963e-11   357.44552 8.868381e-14   9.418048
10335      IL27      16_23 1.421364e-02    81.11968 3.430472e-06  -9.140265
8427      NEGR1       1_46 9.461144e-02    76.49903 2.153387e-05  -8.928461
7515      PSMC3      11_29 6.783380e-03    78.60556 1.586434e-06  -8.866477
      num_eqtl
7227         2
38           1
8727         1
1048         1
8728         1
8068         1
7223         1
1721         1
10189        1
11438        1
10225        1
10271        1
10322        2
7747         1
5341         1
8426         1
11752        1
10335        1
8427         1
7515         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] 0.02136346
       genename region_tag    susie_pip         mu2          PVE          z
7227      MST1R       3_35 0.000000e+00 34543.28743 0.000000e+00 -12.635394
38         RBM6       3_35 0.000000e+00 40475.72984 0.000000e+00  12.536042
8727     ASPHD1      16_24 5.915066e-01   120.67330 2.123700e-04 -11.848514
1048      EFR3B       2_15 1.114961e-08   203.24843 6.742318e-12  11.586593
8728     KCTD13      16_24 6.773020e-02   115.83721 2.334280e-05 -11.490673
8068     INO80E      16_24 1.260053e-02   103.17532 3.868004e-06  11.076716
7223     RNF123       3_35 0.000000e+00 22889.67075 0.000000e+00 -10.959165
1721      MAPK3      16_24 1.145581e-02   103.03163 3.511713e-06  10.880016
10189    ATP2A1      16_23 5.055768e-01   100.96198 1.518684e-04 -10.759014
11438    NPIPB7      16_23 7.272766e-02   100.96337 2.184670e-05  10.509650
10225   SULT1A1      16_23 2.946593e-02    99.06621 8.684967e-06  10.367233
10271  C6orf106       6_28 5.814351e-05   124.59696 2.155416e-08 -10.263559
10322   SULT1A2      16_23 1.683314e-02    95.71737 4.793783e-06 -10.171155
7747     ZNF668      16_24 1.090314e-01    80.22421 2.602433e-05  10.000364
5341       SAE1      19_33 1.095253e-03   100.68705 3.281034e-07   9.848747
8426    C1QTNF4      11_29 6.345703e-03    90.11964 1.701460e-06   9.563515
11752 LINC00461       5_52 8.338963e-11   357.44552 8.868381e-14   9.418048
10335      IL27      16_23 1.421364e-02    81.11968 3.430472e-06  -9.140265
8427      NEGR1       1_46 9.461144e-02    76.49903 2.153387e-05  -8.928461
7515      PSMC3      11_29 6.783380e-03    78.60556 1.586434e-06  -8.866477
      num_eqtl
7227         2
38           1
8727         1
1048         1
8728         1
8068         1
7223         1
1721         1
10189        1
11438        1
10225        1
10271        1
10322        2
7747         1
5341         1
8426         1
11752        1
10335        1
8427         1
7515         1

Sensitivity, specificity and precision for silver standard genes

[1] 41
[1] 22
[1] 4.57565
[1] 7
[1] 225
        genename region_tag susie_pip      mu2        PVE         z num_eqtl
789         SDHA        5_1         1 21042.52 0.06260661  3.012479        1
11293 AC078842.3       7_84         1 19171.30 0.05703927 -3.207993        1
4274     IGHMBP2      11_38         1 31336.96 0.09323508 -4.378813        1
5140       MFAP1      15_16         1 29203.28 0.08688685  4.302998        1
     ctwas       TWAS 
0.00000000 0.07317073 
    ctwas      TWAS 
0.9993340 0.9788773 
     ctwas       TWAS 
0.00000000 0.01333333 

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