LDL - Liver

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Last updated: 2023-02-12

Checks: 5 2

Knit directory: cTWAS_analysis/

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/project2/xinhe/shengqian/cTWAS/cTWAS_analysis/data/	data
/project2/xinhe/shengqian/cTWAS/cTWAS_analysis/code/ctwas_config_b38.R	code/ctwas_config_b38.R

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There are no past versions. Publish this analysis with wflow_publish() to start tracking its development.

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Weight QC

[1] 11502

[1] 2828

  1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19  20 
268 199 136  92 117 181 138  88 114 115 180 165  44  93  84 156 178  33 239  77 
 21  22 
 37  94 

[1] 1

Load ctwas results

Check convergence of parameters

#estimated group prior
estimated_group_prior <- estimated_group_prior_all[,ncol(group_prior_rec)]
print(estimated_group_prior)

      SNP      gene 
9.388e-05 4.225e-02 

#estimated group prior variance
estimated_group_prior_var <- estimated_group_prior_var_all[,ncol(group_prior_var_rec)]
print(estimated_group_prior_var)

  SNP  gene 
28.61 10.17 

#estimated enrichment
estimated_enrichment <- estimated_enrichment_all[ncol(group_prior_var_rec)]
print(estimated_enrichment)

[1] 450.1

#report sample size
print(sample_size)

[1] 343621

#report group size
print(group_size)

    SNP    gene 
8696600    2828 

#estimated group PVE
estimated_group_pve <- estimated_group_pve_all[,ncol(group_prior_rec)]
print(estimated_group_pve)

     SNP     gene 
0.067986 0.003536 

#total PVE
sum(estimated_group_pve)

[1] 0.07152

#attributable PVE
estimated_group_pve/sum(estimated_group_pve)

    SNP    gene 
0.95056 0.04944 

Genes with highest PIPs

#distribution of PIPs
hist(ctwas_gene_res$susie_pip, xlim=c(0,1), main="Distribution of Gene PIPs")

#genes with PIP>0.8 or 20 highest PIPs
head(ctwas_gene_res[order(-ctwas_gene_res$susie_pip),report_cols], max(sum(ctwas_gene_res$susie_pip>0.8), 20))

           genename region_tag susie_pip   mu2       PVE      z num_eqtl
11257        CYP2A6      19_28    0.9902 29.03 8.367e-05  5.407        1
10708        NYNRIN       14_3    0.9880 51.39 1.478e-04  7.679        1
1597           PLTP      20_28    0.9873 36.21 1.040e-04 -5.732        1
6774           PKN3       9_66    0.9844 44.38 1.271e-04 -6.644        1
8817         VPS37D       7_47    0.9783 21.11 6.010e-05 -4.576        1
6615          TMED4       7_32    0.9727 50.56 1.431e-04  9.538        1
NA.313         <NA>      11_12    0.9703 21.32 6.020e-05  4.388        1
9054        SPTY2D1      11_13    0.9591 29.09 8.119e-05 -5.587        1
7809   CTB-50L17.10       19_5    0.9515 19.74 5.467e-05  4.277        1
NA.311         <NA>      6_103    0.9231 40.69 1.093e-04 -6.094        1
7350           BRI3       7_60    0.9214 25.56 6.853e-05 -5.079        1
1320        CWF19L1      10_64    0.9152 31.15 8.297e-05  5.707        1
9156         TMEM64       8_64    0.9101 30.24 8.008e-05  3.169        1
6855       ALDH16A1      19_34    0.9088 25.72 6.802e-05 -4.053        1
3714       SLC2A4RG      20_38    0.8938 28.39 7.386e-05 -5.563        1
NA.310         <NA>       5_78    0.8915 17.27 4.480e-05 -3.848        1
328          SLC4A7       3_20    0.8875 20.36 5.257e-05 -4.181        1
7992       TMEM150A       2_54    0.8744 16.99 4.324e-05  3.718        1
4317           RSG1       1_11    0.8741 18.54 4.716e-05 -4.179        1
2454        ST3GAL4      11_77    0.8733 68.45 1.740e-04 11.734        1
3889         STYXL1       7_48    0.8705 30.45 7.714e-05 -5.633        1
7679          PATL1      11_34    0.8527 17.09 4.240e-05  3.820        1
138            IL32       16_3    0.8427 16.67 4.087e-05  3.544        1
3330         SEC16B       1_87    0.8412 17.87 4.376e-05 -3.767        1
4669          SCYL2      12_59    0.8407 16.92 4.140e-05 -3.564        1
3501          CALD1       7_82    0.8227 17.90 4.286e-05 -3.737        1
9476          CMSS1       3_63    0.8003 18.56 4.323e-05 -3.839        1

Genes with largest effect sizes

#plot PIP vs effect size
plot(ctwas_gene_res$susie_pip, ctwas_gene_res$mu2, xlab="PIP", ylab="mu^2", main="Gene PIPs vs Effect Size")

#genes with 20 largest effect sizes
head(ctwas_gene_res[order(-ctwas_gene_res$mu2),report_cols],20)

       genename region_tag susie_pip      mu2       PVE        z num_eqtl
5797    SLC22A3      6_104 0.000e+00 37695.93 0.000e+00  -6.2246        1
NA.306     <NA>       1_67 2.906e-01  1393.15 1.178e-03 -41.7935        1
4433      PSRC1       1_67 2.974e-01  1346.04 1.165e-03 -41.0871        1
10549   HLA-DMA       6_27 1.102e-04   330.51 1.060e-07  -2.3643        1
2077    ATP13A1      19_15 1.043e-01   280.30 8.506e-05 -18.3960        1
8026      PCSK9       1_34 2.691e-03   193.48 1.515e-06  16.0785        1
5988      FADS1      11_34 4.865e-01   136.38 1.931e-04  12.6748        1
8700        ABO       9_70 1.169e-01   136.29 4.638e-05  12.0997        1
10926     FADS3      11_34 6.932e-02   103.77 2.093e-05  11.0739        1
9251     ZNF329      19_39 7.982e-01    98.82 2.296e-04  10.4360        1
11078   HLA-DOB       6_27 2.389e-03    92.32 6.419e-07  -0.9047        1
9910       RHCE       1_18 5.740e-02    84.90 1.418e-05  10.0287        1
4047    NECTIN2      19_31 0.000e+00    84.36 0.000e+00   5.8246        1
10475    TBKBP1      17_27 1.451e-01    79.57 3.360e-05  -9.5850        1
11016     APOC2      19_31 0.000e+00    78.61 0.000e+00 -12.2066        1
366      PHLPP2      16_38 4.015e-07    73.29 8.564e-11  -8.7039        1
6183       POC5       5_44 2.798e-02    73.07 5.950e-06  10.8623        1
5375     GEMIN7      19_31 0.000e+00    71.85 0.000e+00  12.2666        1
11372     APOC4      19_31 0.000e+00    69.64 0.000e+00  -1.0396        1
6090    CSNK1G3       5_75 5.342e-01    68.85 1.070e-04   8.8808        1

Genes with highest PVE

#genes with 20 highest pve
head(ctwas_gene_res[order(-ctwas_gene_res$PVE),report_cols],20)

       genename region_tag susie_pip     mu2       PVE       z num_eqtl
NA.306     <NA>       1_67    0.2906 1393.15 1.178e-03 -41.793        1
4433      PSRC1       1_67    0.2974 1346.04 1.165e-03 -41.087        1
9251     ZNF329      19_39    0.7982   98.82 2.296e-04  10.436        1
5988      FADS1      11_34    0.4865  136.38 1.931e-04  12.675        1
2454    ST3GAL4      11_77    0.8733   68.45 1.740e-04  11.734        1
10708    NYNRIN       14_3    0.9880   51.39 1.478e-04   7.679        1
6615      TMED4       7_32    0.9727   50.56 1.431e-04   9.538        1
6774       PKN3       9_66    0.9844   44.38 1.271e-04  -6.644        1
NA.311     <NA>      6_103    0.9231   40.69 1.093e-04  -6.094        1
6090    CSNK1G3       5_75    0.5342   68.85 1.070e-04   8.881        1
1597       PLTP      20_28    0.9873   36.21 1.040e-04  -5.732        1
10552      TAP2       6_27    0.5966   58.39 1.014e-04   7.663        1
2077    ATP13A1      19_15    0.1043  280.30 8.506e-05 -18.396        1
11257    CYP2A6      19_28    0.9902   29.03 8.367e-05   5.407        1
1320    CWF19L1      10_64    0.9152   31.15 8.297e-05   5.707        1
2092        SP4       7_19    0.6662   42.56 8.252e-05  -7.429        1
9054    SPTY2D1      11_13    0.9591   29.09 8.119e-05  -5.587        1
9156     TMEM64       8_64    0.9101   30.24 8.008e-05   3.169        1
3889     STYXL1       7_48    0.8705   30.45 7.714e-05  -5.633        1
3714   SLC2A4RG      20_38    0.8938   28.39 7.386e-05  -5.563        1

Genes with largest z scores

#genes with 20 largest z scores
head(ctwas_gene_res[order(-abs(ctwas_gene_res$z)),report_cols],20)

       genename region_tag susie_pip     mu2       PVE       z num_eqtl
NA.306     <NA>       1_67 2.906e-01 1393.15 1.178e-03 -41.793        1
4433      PSRC1       1_67 2.974e-01 1346.04 1.165e-03 -41.087        1
2077    ATP13A1      19_15 1.043e-01  280.30 8.506e-05 -18.396        1
8026      PCSK9       1_34 2.691e-03  193.48 1.515e-06  16.079        1
5988      FADS1      11_34 4.865e-01  136.38 1.931e-04  12.675        1
5375     GEMIN7      19_31 0.000e+00   71.85 0.000e+00  12.267        1
11016     APOC2      19_31 0.000e+00   78.61 0.000e+00 -12.207        1
8700        ABO       9_70 1.169e-01  136.29 4.638e-05  12.100        1
2454    ST3GAL4      11_77 8.733e-01   68.45 1.740e-04  11.734        1
10926     FADS3      11_34 6.932e-02  103.77 2.093e-05  11.074        1
6183       POC5       5_44 2.798e-02   73.07 5.950e-06  10.862        1
9251     ZNF329      19_39 7.982e-01   98.82 2.296e-04  10.436        1
9910       RHCE       1_18 5.740e-02   84.90 1.418e-05  10.029        1
10475    TBKBP1      17_27 1.451e-01   79.57 3.360e-05  -9.585        1
6615      TMED4       7_32 9.727e-01   50.56 1.431e-04   9.538        1
6090    CSNK1G3       5_75 5.342e-01   68.85 1.070e-04   8.881        1
366      PHLPP2      16_38 4.015e-07   73.29 8.564e-11  -8.704        1
10996  HLA-DQB2       6_26 5.260e-02   42.63 6.524e-06  -7.859        1
9071   HLA-DQB1       6_26 5.244e-02   42.15 6.432e-06   7.804        1
10708    NYNRIN       14_3 9.880e-01   51.39 1.478e-04   7.679        1

Comparing z scores and PIPs

#set nominal signifiance threshold for z scores
alpha <- 0.05

#bonferroni adjusted threshold for z scores
sig_thresh <- qnorm(1-(alpha/nrow(ctwas_gene_res)/2), lower=T)

#Q-Q plot for z scores
obs_z <- ctwas_gene_res$z[order(ctwas_gene_res$z)]
exp_z <- qnorm((1:nrow(ctwas_gene_res))/nrow(ctwas_gene_res))

plot(exp_z, obs_z, xlab="Expected z", ylab="Observed z", main="Gene z score Q-Q plot")
abline(a=0,b=1)

#plot z score vs PIP
plot(abs(ctwas_gene_res$z), ctwas_gene_res$susie_pip, xlab="abs(z)", ylab="PIP")
abline(v=sig_thresh, col="red", lty=2)

#number of significant z scores
sum(abs(ctwas_gene_res$z) > sig_thresh)

[1] 92

#proportion of significant z scores
mean(abs(ctwas_gene_res$z) > sig_thresh)

[1] 0.03253

#genes with most significant z scores
head(ctwas_gene_res[order(-abs(ctwas_gene_res$z)),report_cols],20)

       genename region_tag susie_pip     mu2       PVE       z num_eqtl
NA.306     <NA>       1_67 2.906e-01 1393.15 1.178e-03 -41.793        1
4433      PSRC1       1_67 2.974e-01 1346.04 1.165e-03 -41.087        1
2077    ATP13A1      19_15 1.043e-01  280.30 8.506e-05 -18.396        1
8026      PCSK9       1_34 2.691e-03  193.48 1.515e-06  16.079        1
5988      FADS1      11_34 4.865e-01  136.38 1.931e-04  12.675        1
5375     GEMIN7      19_31 0.000e+00   71.85 0.000e+00  12.267        1
11016     APOC2      19_31 0.000e+00   78.61 0.000e+00 -12.207        1
8700        ABO       9_70 1.169e-01  136.29 4.638e-05  12.100        1
2454    ST3GAL4      11_77 8.733e-01   68.45 1.740e-04  11.734        1
10926     FADS3      11_34 6.932e-02  103.77 2.093e-05  11.074        1
6183       POC5       5_44 2.798e-02   73.07 5.950e-06  10.862        1
9251     ZNF329      19_39 7.982e-01   98.82 2.296e-04  10.436        1
9910       RHCE       1_18 5.740e-02   84.90 1.418e-05  10.029        1
10475    TBKBP1      17_27 1.451e-01   79.57 3.360e-05  -9.585        1
6615      TMED4       7_32 9.727e-01   50.56 1.431e-04   9.538        1
6090    CSNK1G3       5_75 5.342e-01   68.85 1.070e-04   8.881        1
366      PHLPP2      16_38 4.015e-07   73.29 8.564e-11  -8.704        1
10996  HLA-DQB2       6_26 5.260e-02   42.63 6.524e-06  -7.859        1
9071   HLA-DQB1       6_26 5.244e-02   42.15 6.432e-06   7.804        1
10708    NYNRIN       14_3 9.880e-01   51.39 1.478e-04   7.679        1

SNPs with highest PIPs

#snps with PIP>0.8 or 20 highest PIPs
head(ctwas_snp_res[order(-ctwas_snp_res$susie_pip),report_cols_snps],
max(sum(ctwas_snp_res$susie_pip>0.8), 20))

                 id region_tag susie_pip       mu2       PVE        z
14605     rs2495502       1_34    1.0000    401.68 1.169e-03   6.2922
71888     rs1042034       2_13    1.0000    261.73 7.617e-04  16.5730
71894      rs934197       2_13    1.0000    413.10 1.202e-03  33.0609
73624      rs780093       2_16    1.0000    198.48 5.776e-04 -14.1426
326578  rs115740542       6_20    1.0000    173.22 5.041e-04 -12.5323
370564   rs60425481      6_104    1.0000 254263.08 7.400e-01  -7.1125
759176  rs113408695      17_39    1.0000    163.07 4.746e-04  12.7688
792455   rs73013176       19_9    1.0000    238.12 6.930e-04 -16.2327
792493  rs137992968       19_9    1.0000    234.44 6.823e-04 -10.7526
795290    rs3794991      19_15    1.0000    501.74 1.460e-03 -21.4921
802596   rs62117204      19_31    1.0000    828.22 2.410e-03 -44.6722
802614  rs111794050      19_31    1.0000    814.02 2.369e-03 -33.5996
802647     rs814573      19_31    1.0000   2381.88 6.932e-03  55.5379
802649  rs113345881      19_31    1.0000    830.63 2.417e-03 -34.3186
802652   rs12721109      19_31    1.0000   1434.60 4.175e-03 -46.3258
897616   rs67138090       6_27    1.0000   2561.39 7.454e-03   4.4111
813183   rs34507316      20_13    1.0000     97.35 2.833e-04  -6.8147
327311     rs454182       6_22    1.0000    151.60 4.412e-04   4.7791
759202    rs8070232      17_39    1.0000    197.65 5.752e-04  -8.0915
71839    rs11679386       2_12    1.0000    168.71 4.910e-04  11.9094
71974     rs1848922       2_13    1.0000    242.15 7.047e-04  25.4123
71897      rs548145       2_13    1.0000    713.12 2.075e-03  33.0860
505608  rs115478735       9_70    1.0000    335.71 9.770e-04  19.0118
497391    rs2437818       9_53    1.0000     81.53 2.373e-04   6.3340
1045619   rs1800961      20_28    1.0000     78.53 2.285e-04  -8.8970
733872   rs12149380      16_38    1.0000    134.20 3.906e-04  -4.1646
758260    rs1801689      17_38    1.0000     87.71 2.553e-04   9.3964
802310   rs73036721      19_30    1.0000     64.83 1.887e-04  -7.7879
428656    rs7012814       8_12    1.0000    100.62 2.928e-04  10.9061
444842    rs4738679       8_45    1.0000    117.23 3.412e-04 -11.6999
278105    rs1499279       5_30    1.0000     68.69 1.999e-04  -8.3746
79689    rs72800939       2_28    1.0000     61.03 1.776e-04  -7.8457
14616    rs10888896       1_34    1.0000    150.41 4.377e-04  11.8938
7420     rs79598313       1_18    1.0000     50.68 1.475e-04   7.0246
443447  rs140753685       8_42    1.0000     61.14 1.779e-04   7.7992
802355   rs62115478      19_30    1.0000    202.52 5.894e-04 -14.3262
55203     rs2807848      1_112    1.0000     61.02 1.776e-04  -7.8828
14575    rs11580527       1_34    1.0000     92.62 2.695e-04 -11.1672
463800   rs13252684       8_83    1.0000    266.94 7.768e-04  11.9644
1033018  rs73045960      19_32    1.0000    159.95 4.655e-04 -12.8179
795321  rs113619686      19_15    1.0000     74.34 2.164e-04   0.5939
326557   rs72834643       6_20    1.0000     53.42 1.555e-04  -6.0487
463797    rs6470359       8_83    1.0000    317.18 9.230e-04   9.6469
813182    rs6075251      20_13    1.0000     69.96 2.036e-04  -2.3298
352856    rs9496567       6_67    1.0000     42.29 1.231e-04  -6.3402
322849   rs11376017       6_13    0.9999     71.92 2.093e-04  -8.5079
702570    rs2070895      15_26    0.9998     63.99 1.862e-04   7.7347
792519    rs4804149      19_10    0.9998     50.25 1.462e-04   6.5194
792572     rs322144      19_10    0.9998     70.10 2.040e-04   3.9466
370652  rs374071816      6_104    0.9998  45729.13 1.330e-01  16.2541
733915   rs57186116      16_38    0.9996     75.01 2.182e-04   7.7146
543351   rs17875416      10_71    0.9995     41.39 1.204e-04  -6.2663
79553   rs139029940       2_27    0.9994     41.05 1.194e-04   6.8150
284557    rs7701166       5_44    0.9993     39.76 1.156e-04  -2.4848
497364    rs2297400       9_53    0.9992     43.99 1.279e-04   6.6057
608882    rs7397189      12_36    0.9992     37.31 1.085e-04  -5.7710
794930    rs2302209      19_14    0.9988     46.79 1.360e-04   6.6360
433174    rs1495743       8_20    0.9986     44.41 1.291e-04  -6.5160
912208     rs662138      6_103    0.9982    124.29 3.611e-04  11.2979
739367    rs2255451      16_48    0.9982     41.34 1.201e-04  -6.3628
463788    rs2980875       8_83    0.9976    596.29 1.731e-03 -22.1022
912140   rs12208357      6_103    0.9974    204.82 5.945e-04  12.2823
14623      rs471705       1_34    0.9973    225.29 6.539e-04  16.2630
792476  rs147985405       19_9    0.9971   2728.60 7.918e-03 -48.9352
585738   rs75542613      11_70    0.9970     38.50 1.117e-04  -6.5344
585733    rs3135506      11_70    0.9966    160.77 4.663e-04  12.3730
383559   rs56130071       7_19    0.9961    107.27 3.110e-04  10.9789
818136   rs76981217      20_24    0.9960     36.88 1.069e-04   7.6925
624874     rs653178      12_67    0.9954    109.75 3.179e-04  11.0501
444810   rs56386732       8_45    0.9947     36.26 1.050e-04  -7.0123
897506    rs9275698       6_27    0.9937   2533.19 7.325e-03  -0.6590
663674    rs3934835      13_62    0.9935     62.74 1.814e-04   7.9439
803515     rs838145      19_33    0.9921    107.70 3.110e-04 -11.8738
141832     rs709149        3_9    0.9918     41.36 1.194e-04  -6.7820
327748    rs3130253       6_23    0.9901     31.47 9.067e-05   5.6415
328533   rs28780090       6_24    0.9888     54.57 1.570e-04   6.8714
818087    rs6029132      20_24    0.9874     42.32 1.216e-04  -6.7625
613248  rs148481241      12_44    0.9856     29.40 8.432e-05   5.0955
148478    rs9834932       3_24    0.9856     72.21 2.071e-04  -8.4816
284498   rs10062361       5_44    0.9849    228.73 6.556e-04  20.3206
733648    rs4396539      16_37    0.9790     29.34 8.360e-05  -5.2329
594365   rs11048034       12_9    0.9746     39.91 1.132e-04   6.1337
79566    rs13430143       2_27    0.9720    100.23 2.835e-04  -3.3445
405771    rs3197597       7_61    0.9711     30.67 8.668e-05  -5.0452
247912  rs114756490      4_100    0.9698     27.78 7.840e-05   4.9889
479716    rs1556516       9_16    0.9670     80.15 2.256e-04  -8.9921
225183    rs1458038       4_54    0.9661     56.62 1.592e-04  -7.4179
628254   rs11057830      12_76    0.9656     27.84 7.822e-05   4.9296
79569     rs4076834       2_27    0.9635    481.67 1.351e-03 -20.1086
326396   rs75080831       6_19    0.9621     62.84 1.759e-04  -7.9067
30636     rs1730862       1_66    0.9608     31.11 8.700e-05  -5.2846
1014613  rs78173576       17_6    0.9599     32.48 9.075e-05  -5.1389
818140   rs73124945      20_24    0.9594     33.14 9.252e-05  -7.7754
390928  rs141379002       7_33    0.9583     27.65 7.712e-05   4.8970
762335    rs4969183      17_44    0.9572     53.00 1.476e-04   7.1693
569362    rs6591179      11_36    0.9569     27.87 7.760e-05   4.8933
327719   rs28986304       6_23    0.9523     44.83 1.242e-04   7.3825
825857   rs62219001       21_2    0.9512     28.05 7.764e-05  -4.9484
471852    rs7024888        9_3    0.9506     27.66 7.653e-05  -5.0558
912244    rs2297374      6_103    0.9401    135.79 3.715e-04 -12.1550
1015731   rs2908806       17_7    0.9348     40.38 1.098e-04  -6.0264
733913    rs9652628      16_38    0.9345    137.95 3.751e-04  11.9505
622967    rs1196760      12_63    0.9316     27.52 7.461e-05  -4.8667
637141    rs1012130      13_10    0.9294     48.67 1.316e-04  -2.7810
355592   rs12199109       6_73    0.9151     27.03 7.200e-05   4.8570
858234   rs16828576       1_16    0.9132     31.35 8.332e-05  -4.7429
510558   rs10905277       10_8    0.9096     29.84 7.899e-05   5.1258
749224  rs117859452      17_17    0.9096     26.40 6.987e-05  -3.8517
543062   rs12244851      10_70    0.9080     40.83 1.079e-04  -4.8831
749133    rs3032928      17_17    0.9063     36.73 9.688e-05   6.1119
729756     rs821840      16_30    0.9063    179.77 4.741e-04 -13.4753
14606     rs1887552       1_34    0.9017    445.83 1.170e-03  -9.8686
792560     rs322125      19_10    0.9010    120.04 3.147e-04  -7.4704
71891    rs78610189       2_13    0.9004     63.88 1.674e-04  -8.3855
198595   rs36205397        4_4    0.9002     43.16 1.131e-04   6.1594
123929    rs7569317      2_120    0.8994     53.30 1.395e-04   7.9007
328556   rs62407548       6_24    0.8949     71.31 1.857e-04   8.2573
497384    rs2777788       9_53    0.8939     67.50 1.756e-04  -5.7370
792486    rs2738447       19_9    0.8869    406.10 1.048e-03  17.7674
821639   rs10641149      20_32    0.8834     29.28 7.526e-05   5.0758
487702   rs11144506       9_35    0.8711     28.85 7.315e-05   5.0427
582002  rs201912654      11_59    0.8697     41.15 1.042e-04  -6.3056
803490   rs62130338      19_33    0.8683     44.66 1.129e-04   8.4694
813163   rs78348000      20_13    0.8676     32.23 8.136e-05   5.2206
284521    rs3843482       5_44    0.8605    444.53 1.113e-03  25.0344
808828   rs74273659       20_5    0.8586     26.73 6.680e-05   4.6468
196808    rs5855544      3_120    0.8514     26.74 6.625e-05  -4.5937
753847    rs4793601      17_28    0.8492     32.24 7.968e-05  -6.2095
361795    rs9321207       6_86    0.8485     32.48 8.020e-05   5.4016
99599   rs138192199       2_69    0.8469     26.63 6.564e-05   4.6708
759187    rs9303012      17_39    0.8457    197.13 4.852e-04   2.2591
816881   rs11167269      20_21    0.8435     62.56 1.536e-04  -7.7950
1035312   rs3764613      19_32    0.8405     33.83 8.276e-05  -4.8164
71691     rs6531234       2_12    0.8380     44.18 1.078e-04  -7.1708
818105    rs6102034      20_24    0.8372    104.13 2.537e-04 -11.1900
40333     rs1795240       1_84    0.8350     27.53 6.689e-05  -4.8462
637133    rs1799955      13_10    0.8345     82.21 1.997e-04  -6.6936
428625  rs117037226       8_11    0.8340     26.40 6.408e-05   4.1922
200820    rs2002574       4_10    0.8312     27.18 6.574e-05  -4.5583
702569  rs139823028      15_26    0.8299     26.72 6.452e-05   3.9898
733853   rs12708919      16_38    0.8283    159.38 3.842e-04  11.3028
1014343  rs55714927       17_6    0.8246     96.78 2.322e-04  -9.6448
833098    rs2835302      21_16    0.8244     27.72 6.649e-05  -4.6537
792529   rs58495388      19_10    0.8213     36.41 8.702e-05   5.5313
834235  rs149577713      21_19    0.8156     33.88 8.041e-05   3.3168
818281   rs11086801      20_25    0.8123    117.70 2.782e-04  10.9752
862519   rs12740374       1_67    0.8102   1568.76 3.699e-03 -41.7935
428667   rs13265179       8_12    0.8086     38.95 9.165e-05  -7.4149
537852   rs10882161      10_59    0.8056     31.26 7.330e-05  -5.4756
499962    rs2762469       9_56    0.8039     26.81 6.273e-05  -4.5317

SNPs with largest effect sizes

#plot PIP vs effect size
#plot(ctwas_snp_res$susie_pip, ctwas_snp_res$mu2, xlab="PIP", ylab="mu^2", main="SNP PIPs vs Effect Size")

#SNPs with 50 largest effect sizes
head(ctwas_snp_res[order(-ctwas_snp_res$mu2),report_cols_snps],50)

                id region_tag susie_pip    mu2       PVE      z
370560   rs3106169      6_104 7.729e-01 254324 5.720e-01 11.139
370561   rs3127598      6_104 4.346e-01 254322 3.217e-01 11.135
370569   rs3106167      6_104 4.047e-01 254321 2.996e-01 11.136
370564  rs60425481      6_104 1.000e+00 254263 7.400e-01 -7.113
370553  rs11755965      6_104 2.269e-05 254243 1.679e-05 11.140
370544  rs12194962      6_104 2.998e-15 253708 2.213e-15 11.106
370562   rs3127597      6_104 4.552e-15 253541 3.359e-15 11.145
370523   rs3119311      6_104 0.000e+00 184266 0.000e+00  8.031
370517   rs3127579      6_104 0.000e+00 134045 0.000e+00  7.568
370511  rs10945658      6_104 0.000e+00 117098 0.000e+00  8.309
370510   rs3119308      6_104 0.000e+00 116814 0.000e+00  8.274
370506   rs3103352      6_104 0.000e+00 116769 0.000e+00  8.522
370502   rs3101821      6_104 0.000e+00 116358 0.000e+00  8.528
370508  rs12205178      6_104 0.000e+00 116144 0.000e+00  8.297
370500 rs148015788      6_104 0.000e+00 114639 0.000e+00  8.351
370611   rs3124784      6_104 0.000e+00  95684 0.000e+00  9.680
370612   rs3127596      6_104 0.000e+00  86712 0.000e+00  9.556
370605   rs3127599      6_104 0.000e+00  86360 0.000e+00  9.259
370575   rs2481030      6_104 0.000e+00  83598 0.000e+00  4.811
370540   rs2504949      6_104 0.000e+00  68992 0.000e+00  2.937
370593    rs388170      6_104 0.000e+00  63823 0.000e+00  3.833
370515    rs316013      6_104 0.000e+00  61217 0.000e+00 -3.002
370516    rs316012      6_104 0.000e+00  60476 0.000e+00 -3.074
370596   rs9355288      6_104 0.000e+00  58810 0.000e+00  6.319
370504    rs610206      6_104 0.000e+00  55899 0.000e+00 -2.944
370505    rs595374      6_104 0.000e+00  55793 0.000e+00 -2.921
370512    rs315995      6_104 0.000e+00  54412 0.000e+00 -3.207
370509    rs543435      6_104 0.000e+00  54203 0.000e+00 -3.250
370558    rs452867      6_104 0.000e+00  50537 0.000e+00 -7.124
370567    rs367334      6_104 0.000e+00  50505 0.000e+00 -7.106
370556    rs600584      6_104 0.000e+00  50497 0.000e+00 -7.113
370555    rs589931      6_104 0.000e+00  50497 0.000e+00 -7.116
370557    rs434953      6_104 0.000e+00  50496 0.000e+00 -7.111
370563    rs380498      6_104 0.000e+00  50495 0.000e+00 -7.115
370531   rs3119312      6_104 0.000e+00  48834 0.000e+00  3.771
370652 rs374071816      6_104 9.998e-01  45729 1.330e-01 16.254
370590   rs2872317      6_104 0.000e+00  44360 0.000e+00  6.746
370587   rs2313453      6_104 0.000e+00  44333 0.000e+00  6.718
370578 rs146184004      6_104 0.000e+00  42572 0.000e+00  6.534
370657   rs4252185      6_104 2.295e-04  42044 2.808e-05 15.878
370581    rs624319      6_104 0.000e+00  41736 0.000e+00 -6.291
370580    rs637614      6_104 0.000e+00  41666 0.000e+00 -6.362
370582    rs486339      6_104 0.000e+00  41385 0.000e+00 -6.311
370527    rs316036      6_104 0.000e+00  40557 0.000e+00 -7.009
370579    rs555754      6_104 0.000e+00  40242 0.000e+00 -6.593
370658  rs12212146      6_104 0.000e+00  32750 0.000e+00 -2.410
370525    rs582280      6_104 0.000e+00  31626 0.000e+00  2.635
370524    rs497039      6_104 0.000e+00  31618 0.000e+00  2.634
370711   rs1247539      6_104 0.000e+00  25553 0.000e+00 -4.294
370608   rs9346818      6_104 0.000e+00  25017 0.000e+00  7.950

SNPs with highest PVE

#SNPs with 50 highest pve
head(ctwas_snp_res[order(-ctwas_snp_res$PVE),report_cols_snps],50)

                 id region_tag susie_pip      mu2       PVE       z
370564   rs60425481      6_104    1.0000 254263.1 0.7399521  -7.113
370560    rs3106169      6_104    0.7729 254323.7 0.5720466  11.139
370561    rs3127598      6_104    0.4346 254322.2 0.3216625  11.135
370569    rs3106167      6_104    0.4047 254321.2 0.2995505  11.136
370652  rs374071816      6_104    0.9998  45729.1 0.1330496  16.254
792476  rs147985405       19_9    0.9971   2728.6 0.0079179 -48.935
897616   rs67138090       6_27    1.0000   2561.4 0.0074541   4.411
897506    rs9275698       6_27    0.9937   2533.2 0.0073252  -0.659
802647     rs814573      19_31    1.0000   2381.9 0.0069317  55.538
802652   rs12721109      19_31    1.0000   1434.6 0.0041749 -46.326
862519   rs12740374       1_67    0.8102   1568.8 0.0036989 -41.793
802649  rs113345881      19_31    1.0000    830.6 0.0024173 -34.319
802596   rs62117204      19_31    1.0000    828.2 0.0024103 -44.672
802614  rs111794050      19_31    1.0000    814.0 0.0023689 -33.600
71897      rs548145       2_13    1.0000    713.1 0.0020753  33.086
463788    rs2980875       8_83    0.9976    596.3 0.0017312 -22.102
795290    rs3794991      19_15    1.0000    501.7 0.0014602 -21.492
79569     rs4076834       2_27    0.9635    481.7 0.0013506 -20.109
71894      rs934197       2_13    1.0000    413.1 0.0012022  33.061
14606     rs1887552       1_34    0.9017    445.8 0.0011699  -9.869
14605     rs2495502       1_34    1.0000    401.7 0.0011690   6.292
284521    rs3843482       5_44    0.8605    444.5 0.0011132  25.034
792486    rs2738447       19_9    0.8869    406.1 0.0010482  17.767
505608  rs115478735       9_70    1.0000    335.7 0.0009770  19.012
792466    rs8102273       19_9    0.5878    542.6 0.0009283 -14.168
463797    rs6470359       8_83    1.0000    317.2 0.0009230   9.647
463800   rs13252684       8_83    1.0000    266.9 0.0007768  11.964
71888     rs1042034       2_13    1.0000    261.7 0.0007617  16.573
71974     rs1848922       2_13    1.0000    242.2 0.0007047  25.412
792455   rs73013176       19_9    1.0000    238.1 0.0006930 -16.233
792493  rs137992968       19_9    1.0000    234.4 0.0006823 -10.753
284498   rs10062361       5_44    0.9849    228.7 0.0006556  20.321
14623      rs471705       1_34    0.9973    225.3 0.0006539  16.263
792463   rs68010235       19_9    0.4122    534.5 0.0006411 -13.919
912140   rs12208357      6_103    0.9974    204.8 0.0005945  12.282
802355   rs62115478      19_30    1.0000    202.5 0.0005894 -14.326
73624      rs780093       2_16    1.0000    198.5 0.0005776 -14.143
759202    rs8070232      17_39    1.0000    197.7 0.0005752  -8.091
326578  rs115740542       6_20    1.0000    173.2 0.0005041 -12.532
71839    rs11679386       2_12    1.0000    168.7 0.0004910  11.909
759187    rs9303012      17_39    0.8457    197.1 0.0004852   2.259
759176  rs113408695      17_39    1.0000    163.1 0.0004746  12.769
729756     rs821840      16_30    0.9063    179.8 0.0004741 -13.475
585733    rs3135506      11_70    0.9966    160.8 0.0004663  12.373
1033018  rs73045960      19_32    1.0000    160.0 0.0004655 -12.818
862515    rs7528419       1_67    0.1009   1566.0 0.0004598 -41.737
327311     rs454182       6_22    1.0000    151.6 0.0004412   4.779
14616    rs10888896       1_34    1.0000    150.4 0.0004377  11.894
309099   rs12657266       5_92    0.7753    177.9 0.0004013  13.895
733872   rs12149380      16_38    1.0000    134.2 0.0003906  -4.165

SNPs with largest z scores

#histogram of (abs) SNP z scores
hist(abs(ctwas_snp_res$z))

#SNPs with 50 largest z scores
head(ctwas_snp_res[order(-abs(ctwas_snp_res$z)),report_cols_snps],50)

                id region_tag susie_pip    mu2       PVE      z
802647    rs814573      19_31 1.000e+00 2381.9 6.932e-03  55.54
792476 rs147985405       19_9 9.971e-01 2728.6 7.918e-03 -48.94
792471  rs73015020       19_9 2.023e-03 2717.0 1.600e-05 -48.80
792469 rs138175288       19_9 6.112e-04 2714.7 4.829e-06 -48.78
792470 rs138294113       19_9 1.421e-04 2711.6 1.121e-06 -48.75
792472  rs77140532       19_9 7.429e-05 2710.5 5.860e-07 -48.74
792473 rs112552009       19_9 1.073e-05 2706.3 8.455e-08 -48.71
792474  rs10412048       19_9 1.558e-05 2707.4 1.227e-07 -48.70
792468  rs55997232       19_9 1.110e-09 2688.4 8.686e-12 -48.52
802652  rs12721109      19_31 1.000e+00 1434.6 4.175e-03 -46.33
802596  rs62117204      19_31 1.000e+00  828.2 2.410e-03 -44.67
802583   rs1551891      19_31 0.000e+00  480.8 0.000e+00 -42.27
862519  rs12740374       1_67 8.102e-01 1568.8 3.699e-03 -41.79
862515   rs7528419       1_67 1.009e-01 1566.0 4.598e-04 -41.74
862526    rs646776       1_67 7.733e-02 1564.4 3.521e-04  41.73
862525    rs629301       1_67 1.311e-02 1560.5 5.953e-05  41.69
862537    rs583104       1_67 4.988e-04 1515.7 2.200e-06  41.09
862540   rs4970836       1_67 4.860e-04 1512.6 2.139e-06  41.05
862542   rs1277930       1_67 5.034e-04 1507.7 2.209e-06  40.98
862543    rs599839       1_67 5.295e-04 1506.9 2.322e-06  40.96
792477  rs17248769       19_9 0.000e+00 1982.9 0.000e+00 -40.84
792478   rs2228671       19_9 0.000e+00 1971.1 0.000e+00 -40.70
862523   rs3832016       1_67 2.529e-04 1462.2 1.076e-06  40.40
862520    rs660240       1_67 2.481e-04 1454.4 1.050e-06  40.29
862538    rs602633       1_67 3.071e-04 1431.8 1.280e-06  39.96
792467   rs9305020       19_9 0.000e+00 1725.0 0.000e+00 -34.84
802643    rs405509      19_31 0.000e+00  967.3 0.000e+00 -34.64
862506   rs4970834       1_67 6.964e-04 1084.7 2.198e-06 -34.62
802649 rs113345881      19_31 1.000e+00  830.6 2.417e-03 -34.32
802567  rs62120566      19_31 0.000e+00 1399.3 0.000e+00 -33.74
802614 rs111794050      19_31 1.000e+00  814.0 2.369e-03 -33.60
71897     rs548145       2_13 1.000e+00  713.1 2.075e-03  33.09
802620   rs4802238      19_31 0.000e+00  981.8 0.000e+00  33.08
71894     rs934197       2_13 1.000e+00  413.1 1.202e-03  33.06
802561 rs188099946      19_31 0.000e+00 1340.9 0.000e+00 -33.04
802631   rs2972559      19_31 0.000e+00 1347.9 0.000e+00  32.29
802555 rs201314191      19_31 0.000e+00 1242.0 0.000e+00 -32.07
862527   rs3902354       1_67 2.775e-04  922.5 7.451e-07  32.00
862516  rs11102967       1_67 2.691e-04  918.6 7.194e-07  31.94
862541   rs4970837       1_67 3.461e-04  915.7 9.223e-07  31.86
802622  rs56394238      19_31 0.000e+00  984.2 0.000e+00  31.55
802599   rs2965169      19_31 0.000e+00  330.2 0.000e+00 -31.38
802623   rs3021439      19_31 0.000e+00  867.7 0.000e+00  31.05
862511    rs611917       1_67 2.277e-04  864.7 5.731e-07 -30.98
71924   rs12997242       2_13 2.482e-12  375.0 2.709e-15  30.82
802630  rs12162222      19_31 0.000e+00 1150.4 0.000e+00  30.50
71898     rs478588       2_13 2.536e-11  659.6 4.867e-14  30.49
802560  rs62119327      19_31 0.000e+00 1091.3 0.000e+00 -30.42
71899   rs56350433       2_13 6.074e-13  349.8 6.183e-16  30.23
71904   rs56079819       2_13 6.068e-13  349.0 6.164e-16  30.19

Session information

sessionInfo()

R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.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] cowplot_1.1.1   ggplot2_3.4.0   workflowr_1.7.0

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0  xfun_0.35         bslib_0.4.1       generics_0.1.3   
 [5] colorspace_2.0-3  vctrs_0.5.1       htmltools_0.5.4   yaml_2.3.6       
 [9] utf8_1.2.2        blob_1.2.3        rlang_1.0.6       jquerylib_0.1.4  
[13] later_1.3.0       pillar_1.8.1      withr_2.5.0       glue_1.6.2       
[17] DBI_1.1.3         bit64_4.0.5       lifecycle_1.0.3   stringr_1.5.0    
[21] munsell_0.5.0     gtable_0.3.1      evaluate_0.19     memoise_2.0.1    
[25] labeling_0.4.2    knitr_1.41        callr_3.7.3       fastmap_1.1.0    
[29] httpuv_1.6.7      ps_1.7.2          fansi_1.0.3       highr_0.9        
[33] Rcpp_1.0.9        promises_1.2.0.1  scales_1.2.1      cachem_1.0.6     
[37] jsonlite_1.8.4    farver_2.1.0      fs_1.5.2          bit_4.0.5        
[41] digest_0.6.31     stringi_1.7.8     processx_3.8.0    dplyr_1.0.10     
[45] getPass_0.2-2     rprojroot_2.0.3   grid_4.1.0        cli_3.4.1        
[49] tools_4.1.0       magrittr_2.0.3    sass_0.4.4        tibble_3.1.8     
[53] RSQLite_2.2.19    whisker_0.4.1     pkgconfig_2.0.3   data.table_1.14.6
[57] assertthat_0.2.1  rmarkdown_2.19    httr_1.4.4        rstudioapi_0.14  
[61] R6_2.5.1          git2r_0.30.1      compiler_4.1.0