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] 11487

   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
1134  801  689  451  561  646  551  431  414  460  695  611  220  384  375  529 
  17   18   19   20   21   22 
 672  184  903  357  131  288 
[1] 9066
[1] 0.78924

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 
0.0080450365 0.0002899309 
    gene      snp 
20.23213 17.56895 
[1] 336107
[1]   11487 7535010
       gene         snp 
0.005562868 0.114194849 
[1]  0.05015945 17.88795499

Genes with highest PIPs

Version Author Date
e6bc169 sq-96 2022-02-13
          genename region_tag susie_pip        mu2          PVE         z
8160         SMAD3      15_31 0.9999995 8015.87282 2.384916e-02 -2.852677
9866          TMIE       3_33 0.9989779   34.99719 1.040187e-04 -7.091659
3378         CCND2       12_4 0.9648998   28.86368 8.286217e-05 -5.119990
9479         NIM1K       5_28 0.9385399 3262.53413 9.110249e-03  5.550554
7777         ZNF12        7_9 0.9363982   27.17655 7.571420e-05  5.127453
13756        NOL12      22_15 0.8990493   61.44780 1.643661e-04 -4.510837
7320          TAL1       1_29 0.7874439   49.34191 1.156001e-04 -6.865849
1678          NINL      20_19 0.7830803   32.87526 7.659455e-05 -5.599931
12851       CYP2A6      19_28 0.7799696   21.54230 4.999105e-05 -3.989619
13574 RP11-108M9.6       1_12 0.7771895   28.35156 6.555809e-05 -4.914590
7010          NBL1       1_13 0.7555923   34.04073 7.652597e-05 -5.638117
4404         TUBG1      17_25 0.7230289   30.27122 6.511904e-05 -5.660250
13759 RP11-823E8.3      12_54 0.7000492  103.65878 2.159022e-04 -6.438012
4137         PODXL       7_80 0.6950352   26.19268 5.416382e-05  4.018009
9422         SOX11        2_4 0.6665243   26.52941 5.260971e-05  4.517012
7829         YWHAZ       8_69 0.6475680   22.77961 4.388884e-05  4.235328
5519         CDH13      16_46 0.6397455   23.81304 4.532570e-05 -4.826363
1132          RRN3      16_15 0.6239131   22.13907 4.109661e-05  4.374275
12949 RP11-566J3.2      14_52 0.6215001   34.21108 6.326019e-05 -5.489252
2821         SENP6       6_52 0.6090897   25.38256 4.599801e-05 -4.618392
      num_eqtl
8160         2
9866         2
3378         1
9479         2
7777         2
13756        2
7320         1
1678         2
12851        1
13574        1
7010         1
4404         1
13759        1
4137         1
9422         1
7829         1
5519         1
1132         1
12949        1
2821         2

Genes with largest effect sizes

Version Author Date
e6bc169 sq-96 2022-02-13
      genename region_tag    susie_pip      mu2          PVE          z
10604  SLC38A3       3_35 0.000000e+00 68425.51 0.000000e+00   6.725828
7846   CCDC171       9_13 0.000000e+00 52440.50 0.000000e+00   7.972850
7671     CAMKV       3_35 0.000000e+00 52028.02 0.000000e+00  -9.574047
2153    PIK3R2      19_14 0.000000e+00 47754.62 0.000000e+00  -7.140312
36        RBM6       3_35 0.000000e+00 41375.93 0.000000e+00  12.536042
7673     MST1R       3_35 0.000000e+00 35329.04 0.000000e+00 -12.622779
9620     STX19       3_59 0.000000e+00 31328.70 0.000000e+00  -5.059656
5542      NOB1      16_37 0.000000e+00 25284.54 0.000000e+00   2.762572
10375     GSAP       7_49 0.000000e+00 24182.56 0.000000e+00   5.119800
5442     MFAP1      15_16 4.268919e-12 23938.26 3.040415e-13   4.302998
7668    RNF123       3_35 0.000000e+00 23402.76 0.000000e+00 -10.957103
5264     TMOD3      15_21 0.000000e+00 22653.47 0.000000e+00  -4.222248
5446    LYSMD2      15_21 0.000000e+00 22304.53 0.000000e+00  -4.402599
1353     WDR76      15_16 0.000000e+00 21497.96 0.000000e+00   4.808984
901       MCM6       2_80 0.000000e+00 18037.55 0.000000e+00  -3.886179
2155     PDE4C      19_14 0.000000e+00 17890.71 0.000000e+00   6.667721
5158   TUBGCP4      15_16 0.000000e+00 16376.38 0.000000e+00   3.554938
1434     MAST3      19_14 0.000000e+00 15938.64 0.000000e+00  -2.208055
9613     NSUN3       3_59 0.000000e+00 15791.55 0.000000e+00   4.755360
8457     LCMT2      15_16 0.000000e+00 14934.90 0.000000e+00  -2.861302
      num_eqtl
10604        1
7846         2
7671         2
2153         1
36           1
7673         2
9620         1
5542         1
10375        3
5442         1
7668         1
5264         1
5446         1
1353         2
901          1
2155         1
5158         2
1434         1
9613         1
8457         1

Genes with highest PVE

          genename region_tag  susie_pip        mu2          PVE          z
8160         SMAD3      15_31 0.99999954 8015.87282 2.384916e-02  -2.852677
9479         NIM1K       5_28 0.93853991 3262.53413 9.110249e-03   5.550554
13498 CTC-498M16.4       5_52 0.05807462 5398.39878 9.327683e-04   7.882989
10849       TTC30B      2_107 0.26101401  752.00020 5.839884e-04  -3.137443
7062         ADPGK      15_34 0.08467030 1200.49261 3.024217e-04   5.925192
13759 RP11-823E8.3      12_54 0.70004918  103.65878 2.159022e-04  -6.438012
10660        SKOR1      15_31 0.60657759   97.95638 1.767834e-04  -9.879755
13756        NOL12      22_15 0.89904930   61.44780 1.643661e-04  -4.510837
7320          TAL1       1_29 0.78744386   49.34191 1.156001e-04  -6.865849
9866          TMIE       3_33 0.99897790   34.99719 1.040187e-04  -7.091659
13962       DHRS11      17_22 0.53374351   61.96358 9.839920e-05  -8.128326
8419        ATXN2L      16_23 0.36166789   77.22963 8.310294e-05 -10.702325
3378         CCND2       12_4 0.96489977   28.86368 8.286217e-05  -5.119990
5575       C18orf8      18_12 0.48218671   57.70858 8.279004e-05   7.477424
1678          NINL      20_19 0.78308033   32.87526 7.659455e-05  -5.599931
7010          NBL1       1_13 0.75559234   34.04073 7.652597e-05  -5.638117
7777         ZNF12        7_9 0.93639821   27.17655 7.571420e-05   5.127453
5380          SUOX      12_35 0.53798979   47.10209 7.539398e-05  -5.190773
385         PHLPP2      16_38 0.57430624   41.84005 7.149212e-05   4.618775
13574 RP11-108M9.6       1_12 0.77718948   28.35156 6.555809e-05  -4.914590
      num_eqtl
8160         2
9479         2
13498        1
10849        1
7062         3
13759        1
10660        2
13756        2
7320         1
9866         2
13962        1
8419         1
3378         1
5575         2
1678         2
7010         1
7777         2
5380         1
385          1
13574        1

Genes with largest z scores

      genename region_tag    susie_pip         mu2          PVE          z
7673     MST1R       3_35 0.0000000000 35329.04340 0.000000e+00 -12.622779
36        RBM6       3_35 0.0000000000 41375.93494 0.000000e+00  12.536042
7668    RNF123       3_35 0.0000000000 23402.76132 0.000000e+00 -10.957103
8554    INO80E      16_24 0.0316645156    99.46356 9.370425e-06  10.886319
8419    ATXN2L      16_23 0.3616678947    77.22963 8.310294e-05 -10.702325
10629     CLN3      16_23 0.0417000087    75.23465 9.334187e-06  10.363250
10875 C6orf106       6_28 0.0000256066   120.40834 9.173411e-09 -10.263559
12178   NPIPB7      16_23 0.0366258145    74.39248 8.106601e-06  10.037986
8218    ZNF668      16_24 0.1121179514    77.18576 2.574748e-05  10.000364
10660    SKOR1      15_31 0.6065775943    97.95638 1.767834e-04  -9.879755
9435  NFATC2IP      16_23 0.0457742783    75.97829 1.034745e-05  -9.863387
4330     ZC3H4      19_33 0.0052482859    98.99347 1.545776e-06   9.848747
1906      KAT8      16_24 0.0170220382    72.06602 3.649762e-06  -9.785239
1905     BCKDK      16_24 0.0124311403    68.64839 2.539006e-06   9.637985
11636   NDUFS3      11_29 0.0131019911    84.88855 3.309092e-06  -9.629039
7671     CAMKV       3_35 0.0000000000 52028.02173 0.000000e+00  -9.574047
8924   C1QTNF4      11_29 0.0113720906    83.81941 2.836007e-06   9.563515
11640      LAT      16_23 0.0724465661    77.05500 1.660891e-05  -9.552834
10852  FAM180B      11_29 0.0108339097    82.28414 2.652307e-06  -9.489956
2550     MTCH2      11_29 0.0105269672    81.10908 2.540359e-06  -9.432202
      num_eqtl
7673         2
36           1
7668         1
8554         2
8419         1
10629        2
10875        1
12178        1
8218         1
10660        2
9435         1
4330         1
1906         1
1905         1
11636        2
7671         2
8924         1
11640        1
10852        1
2550         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] 0.02002263
      genename region_tag    susie_pip         mu2          PVE          z
7673     MST1R       3_35 0.0000000000 35329.04340 0.000000e+00 -12.622779
36        RBM6       3_35 0.0000000000 41375.93494 0.000000e+00  12.536042
7668    RNF123       3_35 0.0000000000 23402.76132 0.000000e+00 -10.957103
8554    INO80E      16_24 0.0316645156    99.46356 9.370425e-06  10.886319
8419    ATXN2L      16_23 0.3616678947    77.22963 8.310294e-05 -10.702325
10629     CLN3      16_23 0.0417000087    75.23465 9.334187e-06  10.363250
10875 C6orf106       6_28 0.0000256066   120.40834 9.173411e-09 -10.263559
12178   NPIPB7      16_23 0.0366258145    74.39248 8.106601e-06  10.037986
8218    ZNF668      16_24 0.1121179514    77.18576 2.574748e-05  10.000364
10660    SKOR1      15_31 0.6065775943    97.95638 1.767834e-04  -9.879755
9435  NFATC2IP      16_23 0.0457742783    75.97829 1.034745e-05  -9.863387
4330     ZC3H4      19_33 0.0052482859    98.99347 1.545776e-06   9.848747
1906      KAT8      16_24 0.0170220382    72.06602 3.649762e-06  -9.785239
1905     BCKDK      16_24 0.0124311403    68.64839 2.539006e-06   9.637985
11636   NDUFS3      11_29 0.0131019911    84.88855 3.309092e-06  -9.629039
7671     CAMKV       3_35 0.0000000000 52028.02173 0.000000e+00  -9.574047
8924   C1QTNF4      11_29 0.0113720906    83.81941 2.836007e-06   9.563515
11640      LAT      16_23 0.0724465661    77.05500 1.660891e-05  -9.552834
10852  FAM180B      11_29 0.0108339097    82.28414 2.652307e-06  -9.489956
2550     MTCH2      11_29 0.0105269672    81.10908 2.540359e-06  -9.432202
      num_eqtl
7673         2
36           1
7668         1
8554         2
8419         1
10629        2
10875        1
12178        1
8218         1
10660        2
9435         1
4330         1
1906         1
1905         1
11636        2
7671         2
8924         1
11640        1
10852        1
2550         1

Sensitivity, specificity and precision for silver standard genes

[1] 41
[1] 24
[1] 4.593787
[1] 6
[1] 230
      genename region_tag susie_pip       mu2          PVE         z num_eqtl
8160     SMAD3      15_31 0.9999995 8015.8728 0.0238491585 -2.852677        2
13756    NOL12      22_15 0.8990493   61.4478 0.0001643661 -4.510837        2
     ctwas       TWAS 
0.00000000 0.04878049 
    ctwas      TWAS 
0.9994766 0.9801099 
      ctwas        TWAS 
0.000000000 0.008695652 

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