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] 11538

   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
1112  837  689  449  566  643  536  429  430  443  690  629  239  387  388  525 
  17   18   19   20   21   22 
 715  186  889  345  129  282 
[1] 8973
[1] 0.7776911

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 
0.002571585 0.000299628 
    gene      snp 
18.14120 17.46535 
[1] 336107
[1]   11538 7535010
       gene         snp 
0.001601474 0.117318375 
[1]  0.2005197 15.2163902

Genes with highest PIPs

Version Author Date
e6bc169 sq-96 2022-02-13
          genename region_tag susie_pip         mu2          PVE         z
4862          HEY2       6_84 1.0000000 34549.59805 1.027934e-01  5.033965
8605         MRPL1       4_52 0.9999963 16661.35849 4.957141e-02  3.486435
1577         ASCC2      22_10 0.9936907  9364.23192 2.768508e-02 -2.618175
3408         CCND2       12_4 0.8929292    28.66336 7.614942e-05 -5.119990
10379          SP1      12_33 0.7523004    25.56065 5.721181e-05 -4.719016
12572         ETV5      3_114 0.6940969    94.99074 1.961660e-04  9.862284
5598       C18orf8      18_12 0.6056280    55.44443 9.990480e-05  7.499899
13830    HIST1H2BE       6_20 0.4700979    30.74571 4.300267e-05 -6.515410
13559 CTC-498M16.4       5_52 0.4675212    53.74913 7.476446e-05  7.705884
6002          ECE2      3_113 0.4447126    29.33132 3.880910e-05 -5.302197
10039        KCNB2       8_53 0.4401104    64.90303 8.498632e-05 -8.225507
1258        KIF16B      20_12 0.4271436    24.80066 3.151807e-05 -4.619896
12886   AP006621.5       11_1 0.4133098    25.00794 3.075219e-05 -4.506344
7888         YWHAZ       8_69 0.3636711    24.51773 2.652843e-05  4.235328
8734          ELP5       17_6 0.3633053    34.12316 3.688445e-05  4.157351
1722        DNAJC5      20_38 0.3632462    23.94724 2.588088e-05 -4.017824
5697        IGLON5      19_35 0.3603914    31.09134 3.333775e-05 -5.403343
1031        IGSF9B      11_83 0.3492111    29.77714 3.093809e-05  2.128452
5546         CDH13      16_46 0.3484128    24.86130 2.577154e-05 -4.826363
11928       HRAT92        7_1 0.3483643    31.52666 3.267638e-05 -3.948331
      num_eqtl
4862         1
8605         1
1577         1
3408         1
10379        1
12572        1
5598         2
13830        1
13559        1
6002         1
10039        1
1258         1
12886        1
7888         1
8734         2
1722         1
5697         1
1031         1
5546         1
11928        3

Genes with largest effect sizes

Version Author Date
e6bc169 sq-96 2022-02-13
          genename region_tag   susie_pip      mu2          PVE         z
7909       CCDC171       9_13 0.000000000 51332.59 0.000000e+00  7.979137
4862          HEY2       6_84 0.999999990 34549.60 1.027934e-01  5.033965
9691         STX19       3_59 0.000000000 30626.13 0.000000e+00 -5.059656
10446         GSAP       7_49 0.000000000 30470.76 0.000000e+00  5.259703
13068 RP11-490G2.2       1_60 0.000000000 30364.43 0.000000e+00  5.044019
8151          LEO1      15_21 0.000551697 27533.18 4.519385e-05  4.602678
5468         MFAP1      15_16 0.000000000 23395.59 0.000000e+00  4.302998
4567       IGHMBP2      11_38 0.000000000 22373.50 0.000000e+00 -4.327505
13777    LINC02019       3_35 0.102353978 22218.87 6.766267e-03 -4.489974
5290         TMOD3      15_21 0.000000000 21923.04 0.000000e+00 -5.411998
11916       CKMT1A      15_16 0.000000000 21583.23 0.000000e+00 -4.115094
1364         WDR76      15_16 0.000000000 21089.81 0.000000e+00  4.775113
2991          CISH       3_35 0.000000000 19958.31 0.000000e+00 -3.798838
1222       C3orf18       3_35 0.000000000 18831.48 0.000000e+00  4.681781
2990         HEMK1       3_35 0.000000000 18831.48 0.000000e+00 -4.681781
3137         PLCL1      2_117 0.000000000 18556.29 0.000000e+00  5.641781
1064         CCNT2       2_80 0.037246905 18352.47 2.033795e-03  3.685900
2179         PDE4C      19_14 0.000000000 18026.01 0.000000e+00  6.593525
8605         MRPL1       4_52 0.999996266 16661.36 4.957141e-02  3.486435
5185       TUBGCP4      15_16 0.000000000 16113.40 0.000000e+00  3.549755
      num_eqtl
7909         1
4862         1
9691         1
10446        1
13068        1
8151         1
5468         1
4567         2
13777        1
5290         1
11916        1
1364         2
2991         1
1222         1
2990         1
3137         1
1064         1
2179         1
8605         1
5185         2

Genes with highest PVE

          genename region_tag   susie_pip         mu2          PVE         z
4862          HEY2       6_84 0.999999990 34549.59805 1.027934e-01  5.033965
8605         MRPL1       4_52 0.999996266 16661.35849 4.957141e-02  3.486435
1577         ASCC2      22_10 0.993690700  9364.23192 2.768508e-02 -2.618175
13777    LINC02019       3_35 0.102353978 22218.86934 6.766267e-03 -4.489974
3071        LANCL1      2_124 0.267843315  4621.80894 3.683115e-03 -3.534889
1064         CCNT2       2_80 0.037246905 18352.47006 2.033795e-03  3.685900
7733         MFSD8       4_84 0.053940655  6711.43827 1.077096e-03  2.512064
12572         ETV5      3_114 0.694096889    94.99074 1.961660e-04  9.862284
10923       TTC30B      2_107 0.071465298   738.10105 1.569399e-04 -3.137443
11912        VPS52       6_28 0.334931364   122.68343 1.222543e-04  1.606101
5598       C18orf8      18_12 0.605628049    55.44443 9.990480e-05  7.499899
10039        KCNB2       8_53 0.440110354    64.90303 8.498632e-05 -8.225507
3408         CCND2       12_4 0.892929201    28.66336 7.614942e-05 -5.119990
13559 CTC-498M16.4       5_52 0.467521204    53.74913 7.476446e-05  7.705884
179          NISCH       3_36 0.119991924   169.37244 6.046683e-05  4.468118
6862         GPR61       1_67 0.253910668    78.14077 5.903113e-05  8.755235
10379          SP1      12_33 0.752300392    25.56065 5.721181e-05 -4.719016
8151          LEO1      15_21 0.000551697 27533.17584 4.519385e-05  4.602678
13830    HIST1H2BE       6_20 0.470097948    30.74571 4.300267e-05 -6.515410
6002          ECE2      3_113 0.444712642    29.33132 3.880910e-05 -5.302197
      num_eqtl
4862         1
8605         1
1577         1
13777        1
3071         1
1064         1
7733         1
12572        1
10923        1
11912        1
5598         2
10039        1
3408         1
13559        1
179          2
6862         1
10379        1
8151         1
13830        1
6002         1

Genes with largest z scores

            genename region_tag    susie_pip        mu2          PVE          z
7736           MST1R       3_35 2.778368e-03 1066.54212 8.816379e-06 -12.646197
38              RBM6       3_35 3.659374e-04  898.09563 9.778040e-07  12.536042
9298          KCTD13      16_24 3.260224e-02  111.56645 1.082190e-05  11.490673
5215           ADCY3       2_16 5.213089e-05  181.05503 2.808201e-08  10.986823
7732          RNF123       3_35 4.331535e-12  814.76736 1.050021e-14 -10.959165
1846           MAPK3      16_24 6.198097e-03   99.06129 1.826774e-06  10.880016
8639          INO80E      16_24 7.196095e-03   95.02103 2.034413e-06  10.733559
12763 RP11-1348G14.4      16_23 7.269926e-02   92.18324 1.993905e-05  10.676318
11175         NPIPB6      16_23 6.407482e-02   94.14672 1.794796e-05 -10.506225
10711           CLN3      16_23 3.078981e-02   89.34064 8.184242e-06  10.452595
9418           NUPR1      16_23 7.177856e-02   98.60480 2.105791e-05 -10.436769
9502        NFATC2IP      16_23 2.728712e-02   87.47261 7.101535e-06 -10.013408
8296          ZNF668      16_24 3.290834e-02   78.12631 7.649372e-06  10.000364
8995         C1QTNF4      11_29 7.823413e-03   95.03242 2.212027e-06   9.961383
12572           ETV5      3_114 6.940969e-01   94.99074 1.961660e-04   9.862284
1938            KAT8      16_24 6.257505e-03   74.20396 1.381499e-06  -9.848191
11718         NDUFS3      11_29 4.101137e-03   85.98951 1.049234e-06  -9.624203
11003        SULT1A2      16_23 8.562947e-03   77.50311 1.974535e-06  -9.620582
11724            LAT      16_23 5.360090e-02   86.33720 1.376869e-05  -9.552834
2577           MTCH2      11_29 3.824449e-03   84.26680 9.588436e-07  -9.551496
      num_eqtl
7736         3
38           1
9298         1
5215         2
7732         1
1846         1
8639         1
12763        1
11175        1
10711        1
9418         2
9502         1
8296         1
8995         2
12572        1
1938         1
11718        1
11003        2
11724        1
2577         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] 0.0208875
            genename region_tag    susie_pip        mu2          PVE          z
7736           MST1R       3_35 2.778368e-03 1066.54212 8.816379e-06 -12.646197
38              RBM6       3_35 3.659374e-04  898.09563 9.778040e-07  12.536042
9298          KCTD13      16_24 3.260224e-02  111.56645 1.082190e-05  11.490673
5215           ADCY3       2_16 5.213089e-05  181.05503 2.808201e-08  10.986823
7732          RNF123       3_35 4.331535e-12  814.76736 1.050021e-14 -10.959165
1846           MAPK3      16_24 6.198097e-03   99.06129 1.826774e-06  10.880016
8639          INO80E      16_24 7.196095e-03   95.02103 2.034413e-06  10.733559
12763 RP11-1348G14.4      16_23 7.269926e-02   92.18324 1.993905e-05  10.676318
11175         NPIPB6      16_23 6.407482e-02   94.14672 1.794796e-05 -10.506225
10711           CLN3      16_23 3.078981e-02   89.34064 8.184242e-06  10.452595
9418           NUPR1      16_23 7.177856e-02   98.60480 2.105791e-05 -10.436769
9502        NFATC2IP      16_23 2.728712e-02   87.47261 7.101535e-06 -10.013408
8296          ZNF668      16_24 3.290834e-02   78.12631 7.649372e-06  10.000364
8995         C1QTNF4      11_29 7.823413e-03   95.03242 2.212027e-06   9.961383
12572           ETV5      3_114 6.940969e-01   94.99074 1.961660e-04   9.862284
1938            KAT8      16_24 6.257505e-03   74.20396 1.381499e-06  -9.848191
11718         NDUFS3      11_29 4.101137e-03   85.98951 1.049234e-06  -9.624203
11003        SULT1A2      16_23 8.562947e-03   77.50311 1.974535e-06  -9.620582
11724            LAT      16_23 5.360090e-02   86.33720 1.376869e-05  -9.552834
2577           MTCH2      11_29 3.824449e-03   84.26680 9.588436e-07  -9.551496
      num_eqtl
7736         3
38           1
9298         1
5215         2
7732         1
1846         1
8639         1
12763        1
11175        1
10711        1
9418         2
9502         1
8296         1
8995         2
12572        1
1938         1
11718        1
11003        2
11724        1
2577         1

Sensitivity, specificity and precision for silver standard genes

[1] 41
[1] 24
[1] 4.59471
[1] 4
[1] 241
     genename region_tag susie_pip       mu2        PVE         z num_eqtl
8605    MRPL1       4_52 0.9999963 16661.358 0.04957141  3.486435        1
1577    ASCC2      22_10 0.9936907  9364.232 0.02768508 -2.618175        1
     ctwas       TWAS 
0.00000000 0.09756098 
    ctwas      TWAS 
0.9996526 0.9794164 
     ctwas       TWAS 
0.00000000 0.01659751 

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