Last updated: 2023-01-26

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html 684d806 sq-96 2023-01-26 update
Rmd 363ce6a sq-96 2023-01-26 update

Weight QC

[1] 48748
[1] 43661

   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
4104 3452 2299 1938 2229 2922 2432 1993 1233 2189 2583 2100 1147 1395 1414 2130 
  17   18   19   20   21   22 
2453  756 1841 1210  708 1133 
[1] 1

Load ctwas results

Check convergence of parameters

Version Author Date
684d806 sq-96 2023-01-26
#estimated group prior
estimated_group_prior <- estimated_group_prior_all[,ncol(group_prior_rec)]
print(estimated_group_prior)
      SNP      gene 
0.0002067 0.0076251 
#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 
17.08 25.87 
#estimated enrichment
estimated_enrichment <- estimated_enrichment_all[ncol(group_prior_var_rec)]
print(estimated_enrichment)
[1] 36.88
#report sample size
print(sample_size)
[1] 350470
#report group size
print(group_size)
    SNP    gene 
8696600   43661 
#estimated group PVE
estimated_group_pve <- estimated_group_pve_all[,ncol(group_prior_rec)]
print(estimated_group_pve)
    SNP    gene 
0.08761 0.02458 
#total PVE
sum(estimated_group_pve)
[1] 0.1122
#attributable PVE
estimated_group_pve/sum(estimated_group_pve)
   SNP   gene 
0.7809 0.2191 

Genes with highest PIPs

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

Version Author Date
684d806 sq-96 2023-01-26
#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         id susie_pip     mu2
21130                      GCNT2        6_9 cg11118520    1.0000 7149.66
44652                     ZBTB22       6_28 cg25191172    0.9909  177.59
10634                       <NA>       6_24 cg05505711    0.9828  164.88
8001                        <NA>       1_41 cg04111102    0.9647  174.01
30125               RP11-14C10.4      15_50 cg16103421    0.9630   35.05
21908                       DPH1       17_2 cg11577151    0.9562   25.06
29469         AC034220.3;SLC22A5       5_79 cg15738769    0.9547  130.81
6808                        <NA>      2_140 cg03472961    0.9519   34.00
11720           AC006126.4;MARK4      19_31 cg06112816    0.9502  270.67
36599                     KDELC2      11_63 cg20058057    0.9450   29.64
17132                        LYN       8_43 cg08894788    0.9424   50.17
44405            VLDLR;VLDLR-AS1        9_3 cg25032030    0.9251   46.75
39536                      KDM4B       19_5 cg21973527    0.9241   30.75
46332                       <NA>      18_11 cg26234723    0.9149   22.92
21856                      PTPRJ      11_29 cg11545521    0.9130   69.71
16593                       <NA>      11_74 cg08637269    0.8979   67.63
26543                       <NA>      10_83 cg14138475    0.8942   35.35
45859                     TTC39C      18_12 cg25952192    0.8834   32.18
33165 PAX8;PAX8-AS1;RP11-65I12.1       2_67 cg17774569    0.8816   36.18
34842                     SPTLC2      14_36 cg18872420    0.8735   30.35
30365                ATXN7;THOC7       3_43 cg16258503    0.8589   24.00
35811                     GPRIN3       4_60 cg19537443    0.8527   26.82
16511                       SMG9      19_30 cg08581076    0.8489   34.87
44630                      VAMP5       2_54 cg25178838    0.8165   37.39
34253                       CD82      11_27 cg18496383    0.8147   24.35
38057                      PADI1       1_12 cg21010178    0.8142   23.65
44782                       <NA>      21_18 cg25269340    0.8139   60.02
32216                       EHD4      15_15 cg17244218    0.8125  108.37
12790                     GPR116       6_35 cg06673956    0.8107   33.74
            PVE       z num_eqtl
21130 2.040e-02  -3.928        1
44652 5.021e-04   9.566        1
10634 4.624e-04  -1.928        1
8001  4.790e-04 -16.175        1
30125 9.631e-05   5.765        1
21908 6.838e-05  -4.388        1
29469 3.563e-04  13.657        1
6808  9.236e-05  -7.559        1
11720 7.339e-04  14.933        1
36599 7.991e-05  -6.197        1
17132 1.349e-04   7.116        1
44405 1.234e-04   6.429        1
39536 8.108e-05  -5.487        1
46332 5.983e-05  -4.062        1
21856 1.816e-04  -9.930        1
16593 1.733e-04   8.437        1
26543 9.020e-05  -5.918        1
45859 8.112e-05   4.551        1
33165 9.101e-05   6.672        1
34842 7.563e-05   2.576        1
30365 5.882e-05  -4.033        1
35811 6.525e-05  -4.645        1
16511 8.447e-05   4.701        1
44630 8.712e-05  -5.035        1
34253 5.661e-05   4.524        1
38057 5.495e-05  -4.362        1
44782 1.394e-04  -7.733        1
32216 2.512e-04 -12.597        1
12790 7.805e-05   5.585        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")

Version Author Date
684d806 sq-96 2023-01-26
#genes with 20 largest effect sizes
head(ctwas_gene_res[order(-ctwas_gene_res$mu2),report_cols],20)
             genename region_tag         id susie_pip   mu2    PVE        z
41552             LSS      21_24 cg23289605         0 15995 0.0000  -4.8444
18868             LSS      21_24 cg09831081         0 13275 0.0000  -5.2615
22244            PCNT      21_24 cg11764399         0  9266 0.0000   4.5844
21130           GCNT2        6_9 cg11118520         1  7150 0.0204  -3.9282
26726            PCNT      21_24 cg14233374         0  6896 0.0000   4.9575
20725            PCNT      21_24 cg10878966         0  6314 0.0000   5.5785
5838             PCNT      21_24 cg02959939         0  6302 0.0000   5.5187
32742       HCP5;MICA       6_25 cg17529716         0  5615 0.0000  11.2491
18123            YBEY      21_24 cg09417038         0  5411 0.0000  -0.9051
23528            <NA>      21_24 cg12516959         0  5258 0.0000  -0.8848
1720             <NA>      21_24 cg00815214         0  5258 0.0000  -0.8848
43386            <NA>       6_25 cg24439364         0  4395 0.0000  10.8185
1282             <NA>      21_24 cg00612595         0  3936 0.0000  -0.9678
48178  HCP5;LINC01149       6_25 cg27326026         0  3767 0.0000  12.0717
32640       HCP5;MICA       6_25 cg17476405         0  3416 0.0000  14.4636
33606  LSS;MCM3AP-AS1      21_24 cg18069493         0  3406 0.0000   4.0912
14245       HCP5;MICA       6_25 cg07376033         0  3331 0.0000  11.7810
22003            PCNT      21_24 cg11628223         0  2979 0.0000  -1.7442
41         RNU6-1133P       6_25 cg00020172         0  2921 0.0000 -28.4773
47373 HCP5;MICA;Y_RNA       6_25 cg26846810         0  2850 0.0000   6.9007
      num_eqtl
41552        1
18868        1
22244        1
21130        1
26726        1
20725        1
5838         1
32742        1
18123        1
23528        1
1720         1
43386        1
1282         1
48178        1
32640        1
33606        1
14245        1
22003        1
41           1
47373        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         id susie_pip     mu2       PVE
21130              GCNT2        6_9 cg11118520    1.0000 7149.66 0.0204002
14343              PSMD3      17_23 cg07427276    0.7984  622.59 0.0014183
11720   AC006126.4;MARK4      19_31 cg06112816    0.9502  270.67 0.0007339
24271   XXbac-BPG308K3.6       6_22 cg12914966    0.7554  321.11 0.0006921
44652             ZBTB22       6_28 cg25191172    0.9909  177.59 0.0005021
13981               CHD7       8_46 cg07228241    0.7942  212.30 0.0004811
8001                <NA>       1_41 cg04111102    0.9647  174.01 0.0004790
10634               <NA>       6_24 cg05505711    0.9828  164.88 0.0004624
29469 AC034220.3;SLC22A5       5_79 cg15738769    0.9547  130.81 0.0003563
9793               ZPBP2      17_23 cg05057505    0.6335  189.00 0.0003416
42089   MSH5;MSH5-SAPCD1       6_26 cg23634079    0.3764  309.02 0.0003319
30848          C2;ZBTB12       6_26 cg16505946    0.3764  309.02 0.0003319
46716               <NA>      17_23 cg26458775    0.1714  619.42 0.0003030
29677              PREX1      20_30 cg15849237    0.6005  162.21 0.0002780
32216               EHD4      15_15 cg17244218    0.8125  108.37 0.0002512
21856              PTPRJ      11_29 cg11545521    0.9130   69.71 0.0001816
16593               <NA>      11_74 cg08637269    0.8979   67.63 0.0001733
38255              PREX1      20_30 cg21145944    0.3599  163.39 0.0001678
47128               REST       4_41 cg26694713    0.7433   78.03 0.0001655
4819             PAK2;U4      3_121 cg02455773    0.5334  106.62 0.0001623
            z num_eqtl
21130  -3.928        1
14343 -37.218        1
11720  14.933        1
24271  19.798        1
44652   9.566        1
13981   2.826        1
8001  -16.175        1
10634  -1.928        1
29469  13.657        1
9793   23.719        1
42089  26.924        1
30848 -26.924        1
46716 -37.059        1
29677  -2.590        1
32216 -12.597        1
21856  -9.930        1
16593   8.437        1
38255   2.394        1
47128  -9.062        1
4819    9.125        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         id susie_pip    mu2
14343                          PSMD3      17_23 cg07427276 7.984e-01  622.6
46716                           <NA>      17_23 cg26458775 1.714e-01  619.4
32508                     MED24;THRA      17_23 cg17401724 4.598e-10  406.2
31946                          HLA-C       6_25 cg17096289 0.000e+00  846.3
41                        RNU6-1133P       6_25 cg00020172 0.000e+00 2920.5
6981                   MED24;MIR6884      17_23 cg03568305 6.590e-10  350.2
6598                   MED24;MIR6884      17_23 cg03367679 6.590e-10  350.2
9762                            TNXB       6_26 cg05045332 1.110e-16  417.9
11743                           <NA>      17_23 cg06123174 8.195e-08  294.0
9784                       APOM;BAG6       6_26 cg05053818 0.000e+00  445.5
46204                          GSDMA      17_23 cg26162295 6.643e-11  262.9
26619                         SKIV2L       6_26 cg14178705 0.000e+00  420.5
44201                          GSDMA      17_23 cg24910161 5.043e-11  237.5
18438 HLA-B;HLA-C;XXbac-BPG248L24.12       6_25 cg09588770 0.000e+00  858.0
42089               MSH5;MSH5-SAPCD1       6_26 cg23634079 3.764e-01  309.0
30848                      C2;ZBTB12       6_26 cg16505946 3.764e-01  309.0
13216                          BTNL2       6_26 cg06871764 0.000e+00  397.3
44275                           <NA>       6_26 cg24965496 0.000e+00  446.6
31319                        HLA-DRA       6_26 cg16753237 0.000e+00  300.2
39715                           <NA>       6_25 cg22110654 6.433e-10  796.6
            PVE      z num_eqtl
14343 1.418e-03 -37.22        1
46716 3.030e-04 -37.06        1
32508 5.330e-13 -30.92        1
31946 0.000e+00  28.80        1
41    0.000e+00 -28.48        1
6981  6.584e-13  28.44        1
6598  6.584e-13  28.44        1
9762  1.324e-19 -28.30        1
11743 6.875e-11  28.01        1
9784  0.000e+00  27.89        1
46204 4.983e-14 -27.87        1
26619 0.000e+00 -27.59        1
44201 3.418e-14 -27.47        1
18438 0.000e+00  27.12        1
42089 3.319e-04  26.92        1
30848 3.319e-04 -26.92        1
13216 0.000e+00  26.79        1
44275 0.000e+00  26.43        1
31319 0.000e+00  26.11        1
39715 1.462e-12 -25.85        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)

Version Author Date
684d806 sq-96 2023-01-26
#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)

Version Author Date
684d806 sq-96 2023-01-26
#number of significant z scores
sum(abs(ctwas_gene_res$z) > sig_thresh)
[1] 1431
#proportion of significant z scores
mean(abs(ctwas_gene_res$z) > sig_thresh)
[1] 0.03278
#genes with most significant z scores
head(ctwas_gene_res[order(-abs(ctwas_gene_res$z)),report_cols],20)
                            genename region_tag         id susie_pip    mu2
14343                          PSMD3      17_23 cg07427276 7.984e-01  622.6
46716                           <NA>      17_23 cg26458775 1.714e-01  619.4
32508                     MED24;THRA      17_23 cg17401724 4.598e-10  406.2
31946                          HLA-C       6_25 cg17096289 0.000e+00  846.3
41                        RNU6-1133P       6_25 cg00020172 0.000e+00 2920.5
6981                   MED24;MIR6884      17_23 cg03568305 6.590e-10  350.2
6598                   MED24;MIR6884      17_23 cg03367679 6.590e-10  350.2
9762                            TNXB       6_26 cg05045332 1.110e-16  417.9
11743                           <NA>      17_23 cg06123174 8.195e-08  294.0
9784                       APOM;BAG6       6_26 cg05053818 0.000e+00  445.5
46204                          GSDMA      17_23 cg26162295 6.643e-11  262.9
26619                         SKIV2L       6_26 cg14178705 0.000e+00  420.5
44201                          GSDMA      17_23 cg24910161 5.043e-11  237.5
18438 HLA-B;HLA-C;XXbac-BPG248L24.12       6_25 cg09588770 0.000e+00  858.0
42089               MSH5;MSH5-SAPCD1       6_26 cg23634079 3.764e-01  309.0
30848                      C2;ZBTB12       6_26 cg16505946 3.764e-01  309.0
13216                          BTNL2       6_26 cg06871764 0.000e+00  397.3
44275                           <NA>       6_26 cg24965496 0.000e+00  446.6
31319                        HLA-DRA       6_26 cg16753237 0.000e+00  300.2
39715                           <NA>       6_25 cg22110654 6.433e-10  796.6
            PVE      z num_eqtl
14343 1.418e-03 -37.22        1
46716 3.030e-04 -37.06        1
32508 5.330e-13 -30.92        1
31946 0.000e+00  28.80        1
41    0.000e+00 -28.48        1
6981  6.584e-13  28.44        1
6598  6.584e-13  28.44        1
9762  1.324e-19 -28.30        1
11743 6.875e-11  28.01        1
9784  0.000e+00  27.89        1
46204 4.983e-14 -27.87        1
26619 0.000e+00 -27.59        1
44201 3.418e-14 -27.47        1
18438 0.000e+00  27.12        1
42089 3.319e-04  26.92        1
30848 3.319e-04 -26.92        1
13216 0.000e+00  26.79        1
44275 0.000e+00  26.43        1
31319 0.000e+00  26.11        1
39715 1.462e-12 -25.85        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        id.1 susie_pip      mu2       PVE
31705     rs6679677       1_70   rs6679677    1.0000   146.55 4.182e-04
58478    rs10803164      1_122  rs10803164    1.0000   186.85 5.331e-04
62820    rs12239046      1_131  rs12239046    1.0000    99.44 2.837e-04
115498    rs3835963      2_110   rs3835963    1.0000   107.56 3.069e-04
218483    rs1371794       4_51   rs1371794    1.0000   476.03 1.358e-03
221306  rs529050451       4_56 rs529050451    1.0000   708.60 2.022e-03
377037   rs56388170       7_24  rs56388170    1.0000   369.05 1.053e-03
396284   rs79912251       7_56  rs79912251    1.0000   145.07 4.139e-04
628523   rs79490353       13_7  rs79490353    1.0000   192.35 5.488e-04
777917   rs12461480       19_4  rs12461480    1.0000   215.36 6.145e-04
825443   rs13049759      21_24  rs13049759    1.0000 19341.21 5.519e-02
825445   rs13049893      21_24  rs13049893    1.0000 19430.21 5.544e-02
868195   rs34599082       1_78  rs34599082    1.0000   177.67 5.070e-04
934104  rs200599211       5_79 rs200599211    1.0000  1818.82 5.190e-03
979576  rs201369106       6_25 rs201369106    1.0000 12076.72 3.446e-02
1147212      rs4760      19_30      rs4760    1.0000   307.26 8.767e-04
72545      rs780093       2_16    rs780093    1.0000   137.29 3.917e-04
9489      rs3917932       1_22   rs3917932    1.0000   209.91 5.990e-04
396257     rs740047       7_56    rs740047    1.0000    84.84 2.421e-04
321991   rs41258084       6_27  rs41258084    1.0000   189.92 5.419e-04
958381    rs1233380       6_23   rs1233380    1.0000   223.44 6.376e-04
868194      rs12075       1_78     rs12075    1.0000    95.46 2.724e-04
437157    rs4738814       8_46   rs4738814    1.0000   235.41 6.717e-04
461756    rs7462429       8_92   rs7462429    1.0000    95.48 2.724e-04
427615    rs9644063       8_24   rs9644063    1.0000    80.16 2.287e-04
376898     rs177448       7_23    rs177448    1.0000    65.96 1.882e-04
979803    rs9267123       6_25   rs9267123    1.0000   869.07 2.480e-03
732773    rs9914577       17_3   rs9914577    1.0000    94.23 2.689e-04
613910   rs17041439      12_61  rs17041439    1.0000    51.74 1.476e-04
211431     rs218239       4_39    rs218239    1.0000    69.81 1.992e-04
974399    rs2524079       6_25   rs2524079    1.0000  2259.54 6.447e-03
301092    rs1042711       5_87   rs1042711    1.0000    47.90 1.367e-04
322031   rs73412964       6_27  rs73412964    1.0000    77.91 2.223e-04
63028    rs66858280      1_131  rs66858280    1.0000    50.47 1.440e-04
435508  rs140753685       8_42 rs140753685    1.0000    46.21 1.319e-04
576182    rs2852801      11_67   rs2852801    1.0000    50.90 1.452e-04
115472   rs77969163      2_109  rs77969163    1.0000    82.43 2.352e-04
716797   rs12926510      16_24  rs12926510    1.0000   125.48 3.580e-04
461695   rs56114972       8_92  rs56114972    1.0000    42.94 1.225e-04
617055     rs653178      12_67    rs653178    1.0000   573.76 1.637e-03
980873    rs2229094       6_25   rs2229094    1.0000  1485.75 4.239e-03
111332    rs2140046      2_102   rs2140046    1.0000   132.04 3.768e-04
584675    rs1800692       12_7   rs1800692    1.0000    40.22 1.147e-04
497983  rs115478735       9_70 rs115478735    1.0000   127.90 3.649e-04
806172    rs6072084      20_24   rs6072084    1.0000    74.43 2.124e-04
320540    rs1266074       6_26   rs1266074    1.0000   160.57 4.581e-04
379586    rs2700943       7_26   rs2700943    1.0000    53.33 1.522e-04
8108      rs4409706       1_20   rs4409706    1.0000    42.79 1.221e-04
353139     rs210942       6_89    rs210942    1.0000    68.49 1.954e-04
523143     rs748113      10_48    rs748113    1.0000    43.31 1.236e-04
777908    rs2041128       19_4   rs2041128    0.9999   163.61 4.668e-04
729549   rs11641197      16_49  rs11641197    0.9999    54.06 1.543e-04
523156    rs2166632      10_48   rs2166632    0.9999    38.01 1.084e-04
496491   rs13289095       9_66  rs13289095    0.9999    46.77 1.334e-04
379591   rs58130365       7_26  rs58130365    0.9999    40.61 1.159e-04
320502   rs17709192       6_21  rs17709192    0.9999    51.71 1.475e-04
751350    rs3826288      17_43   rs3826288    0.9999    45.77 1.306e-04
314127     rs630258        6_7    rs630258    0.9998    51.76 1.476e-04
221253    rs6814526       4_56   rs6814526    0.9998   309.12 8.818e-04
296841    rs4705986       5_80   rs4705986    0.9998    36.84 1.051e-04
770954  rs144596877      18_35 rs144596877    0.9998    35.03 9.994e-05
457576   rs60379390       8_85  rs60379390    0.9997   121.13 3.455e-04
766738    rs1025685      18_28   rs1025685    0.9997    53.87 1.537e-04
969114    rs3131063       6_24   rs3131063    0.9995   180.87 5.158e-04
720077     rs291040      16_30    rs291040    0.9995    43.56 1.242e-04
437188    rs3763591       8_46   rs3763591    0.9994   141.79 4.044e-04
609950    rs4842610      12_53   rs4842610    0.9993    73.64 2.100e-04
106994   rs59483741       2_91  rs59483741    0.9992    42.27 1.205e-04
506740     rs553304      10_14    rs553304    0.9992    35.45 1.011e-04
316759    rs1322599       6_13   rs1322599    0.9991    64.29 1.833e-04
406898    rs9649546       7_80   rs9649546    0.9986    47.87 1.364e-04
320525    rs2736155       6_26   rs2736155    0.9985   279.53 7.964e-04
406908     rs205721       7_80    rs205721    0.9984    35.96 1.024e-04
545506    rs7111092       11_7   rs7111092    0.9981    32.36 9.216e-05
442581    rs1430828       8_57   rs1430828    0.9981    33.93 9.663e-05
576191     rs238910      11_67    rs238910    0.9980   102.76 2.926e-04
656688     rs383599      13_62    rs383599    0.9980    47.36 1.349e-04
628525    rs7989654       13_7   rs7989654    0.9979   126.67 3.607e-04
806136   rs56206139      20_24  rs56206139    0.9975    32.74 9.319e-05
730241   rs72807046      16_50  rs72807046    0.9975    37.64 1.071e-04
617243    rs7970581      12_68   rs7970581    0.9975    32.75 9.320e-05
826077     rs390109       22_2    rs390109    0.9967    32.73 9.309e-05
25283    rs12130551       1_56  rs12130551    0.9966    31.80 9.042e-05
324927   rs11965885       6_33  rs11965885    0.9965    30.66 8.717e-05
360634   rs11759145      6_103  rs11759145    0.9963    34.94 9.933e-05
309233    rs2594836      5_104   rs2594836    0.9962   131.19 3.729e-04
301808   rs74995440       5_89  rs74995440    0.9955    29.79 8.461e-05
9492      rs3917912       1_22   rs3917912    0.9955    70.14 1.992e-04
1030785     rs14408       11_1     rs14408    0.9954   194.52 5.525e-04
584698    rs2286599       12_7   rs2286599    0.9953    77.11 2.190e-04
211458     rs723585       4_40    rs723585    0.9948    70.99 2.015e-04
791644  rs201074739      19_35 rs201074739    0.9945    30.16 8.559e-05
471562    rs2518722       9_16   rs2518722    0.9941    79.95 2.268e-04
202261  rs112783548       4_21 rs112783548    0.9937    28.71 8.141e-05
743011   rs68017435      17_26  rs68017435    0.9933    29.43 8.340e-05
734895  rs112315122       17_7 rs112315122    0.9932    35.19 9.972e-05
530091   rs17109928      10_60  rs17109928    0.9929    36.03 1.021e-04
423516   rs79690602       8_16  rs79690602    0.9925    27.74 7.856e-05
718211    rs7205341      16_27   rs7205341    0.9925    29.24 8.279e-05
10181     rs6690335       1_24   rs6690335    0.9922    41.18 1.166e-04
227127   rs35518360       4_67  rs35518360    0.9922    30.66 8.680e-05
227815    rs1548483       4_69   rs1548483    0.9919    41.53 1.176e-04
1054962   rs9332865      11_71   rs9332865    0.9918    41.12 1.164e-04
397773    rs1045916       7_60   rs1045916    0.9917    35.74 1.011e-04
695299   rs16947844      15_29  rs16947844    0.9916    70.18 1.986e-04
678759   rs67868394      14_46  rs67868394    0.9910    31.99 9.046e-05
125689   rs16858744      2_129  rs16858744    0.9906    29.89 8.447e-05
368103    rs2462661        7_9   rs2462661    0.9896    40.60 1.146e-04
475470    rs7042042       9_25   rs7042042    0.9895    27.47 7.755e-05
206382   rs75384208       4_30  rs75384208    0.9893    40.40 1.140e-04
483938    rs7863057       9_45   rs7863057    0.9882    43.22 1.219e-04
396361    rs7785869       7_57   rs7785869    0.9860    30.43 8.562e-05
2809     rs10864368        1_6  rs10864368    0.9844    36.92 1.037e-04
77564    rs10604697       2_26  rs10604697    0.9843    28.65 8.047e-05
82036    rs72804694       2_36  rs72804694    0.9842    33.03 9.275e-05
697841     rs876383      15_35    rs876383    0.9819    27.19 7.618e-05
1090478 rs138682554      15_42 rs138682554    0.9789    54.27 1.516e-04
753564   rs35967347      17_47  rs35967347    0.9786    33.03 9.223e-05
798683    rs1997814       20_8   rs1997814    0.9777    30.62 8.541e-05
171334   rs11721161       3_79  rs11721161    0.9767    40.57 1.131e-04
546677    rs4910421       11_9   rs4910421    0.9759    34.83 9.697e-05
188427    rs6782470      3_114   rs6782470    0.9755    26.41 7.350e-05
34996      rs512645       1_79    rs512645    0.9752    30.34 8.443e-05
868196      rs13962       1_78     rs13962    0.9752    58.56 1.630e-04
154686   rs17737336       3_48  rs17737336    0.9723    28.87 8.010e-05
377034   rs12113964       7_24  rs12113964    0.9719    36.67 1.017e-04
309184   rs10054235      5_104  rs10054235    0.9718    25.89 7.179e-05
742719   rs76714145      17_25  rs76714145    0.9712    29.08 8.059e-05
896157   rs17715343       2_97  rs17715343    0.9703    37.60 1.041e-04
775807   rs41506447      18_45  rs41506447    0.9702    25.37 7.022e-05
580061   rs34516251      11_80  rs34516251    0.9702    86.20 2.386e-04
748603    rs1801689      17_38   rs1801689    0.9697    25.62 7.087e-05
7235     rs10751725       1_19  rs10751725    0.9695    39.93 1.105e-04
105084   rs16858573       2_85  rs16858573    0.9690    81.52 2.254e-04
115491     rs155136      2_110    rs155136    0.9679    38.46 1.062e-04
666760  rs545787745      14_19 rs545787745    0.9678    25.20 6.959e-05
442541   rs56080040       8_56  rs56080040    0.9661    82.22 2.266e-04
742575     rs665268      17_25    rs665268    0.9657    42.98 1.184e-04
597984   rs80325942      12_30  rs80325942    0.9652    31.29 8.617e-05
868188   rs41264467       1_78  rs41264467    0.9647    37.87 1.043e-04
134685   rs35516956        3_3  rs35516956    0.9634    25.52 7.014e-05
572215  rs117594293      11_58 rs117594293    0.9629    28.74 7.897e-05
78782    rs11125040       2_28  rs11125040    0.9609    29.08 7.972e-05
787395    rs2194067      19_24   rs2194067    0.9586    28.64 7.833e-05
634076    rs2404726      13_19   rs2404726    0.9585    24.97 6.830e-05
399732    rs2470932       7_65   rs2470932    0.9572    25.09 6.852e-05
850036  rs182050989       1_18 rs182050989    0.9569    62.30 1.701e-04
35287    rs61804205       1_79  rs61804205    0.9557    57.99 1.581e-04
658620    rs9323580       14_4   rs9323580    0.9553   144.36 3.935e-04
655446    rs7991343      13_60   rs7991343    0.9548    26.98 7.352e-05
717874   rs34294937      16_27  rs34294937    0.9547    26.53 7.226e-05
557710  rs184267612      11_31 rs184267612    0.9541    28.69 7.809e-05
1157394   rs1015022      21_18   rs1015022    0.9540    47.98 1.306e-04
314121     rs585312        6_7    rs585312    0.9525    30.85 8.386e-05
407931    rs2347699       7_82   rs2347699    0.9490    31.56 8.545e-05
619609   rs76548188      12_74  rs76548188    0.9466    46.98 1.269e-04
952042   rs35789010       6_19  rs35789010    0.9459    81.40 2.197e-04
456525   rs12550442       8_83  rs12550442    0.9452    29.61 7.986e-05
58154     rs4626924      1_121   rs4626924    0.9447    47.84 1.290e-04
729892    rs7197027      16_50   rs7197027    0.9409    33.82 9.078e-05
794200  rs142236969      19_38 rs142236969    0.9407    25.08 6.731e-05
207362    rs4240247       4_31   rs4240247    0.9403    45.27 1.215e-04
339574   rs11757155       6_61  rs11757155    0.9389    51.60 1.382e-04
535580   rs76059302      10_70  rs76059302    0.9375    28.56 7.639e-05
320571  rs115487693       6_26 rs115487693    0.9372   182.55 4.882e-04
731521  rs111172648      16_53 rs111172648    0.9352    33.44 8.923e-05
620644   rs61955114      12_75  rs61955114    0.9350    38.34 1.023e-04
48861    rs10793741      1_104  rs10793741    0.9325    28.40 7.556e-05
49375     rs2724384      1_105   rs2724384    0.9323    95.42 2.538e-04
952603   rs74537235       6_22  rs74537235    0.9305    60.70 1.612e-04
484266    rs6479586       9_46   rs6479586    0.9282    24.23 6.416e-05
464528   rs10974716        9_5  rs10974716    0.9279    34.97 9.259e-05
607240    rs4842318      12_48   rs4842318    0.9278    28.28 7.488e-05
217915    rs7697091       4_50   rs7697091    0.9275    85.28 2.257e-04
412146  rs140190591       7_92 rs140190591    0.9267    25.21 6.666e-05
318103   rs10806918       6_15  rs10806918    0.9266    27.63 7.306e-05
582018    rs2017948      11_83   rs2017948    0.9265    23.83 6.300e-05
779131    rs4804815       19_7   rs4804815    0.9241    62.77 1.655e-04
319081   rs34492438       6_17  rs34492438    0.9234    25.42 6.698e-05
598993    rs3759178      12_32   rs3759178    0.9203    25.02 6.571e-05
422373    rs4386942       8_14   rs4386942    0.9195    32.48 8.521e-05
530143   rs61886179      10_61  rs61886179    0.9189    30.84 8.085e-05
928994    rs2853677        5_2   rs2853677    0.9180    39.92 1.046e-04
318840  rs115557837       6_16 rs115557837    0.9171    25.72 6.730e-05
711583   rs78083064      16_12  rs78083064    0.9147    23.78 6.207e-05
738239     rs941446      17_15    rs941446    0.9133    59.48 1.550e-04
292988      rs11064       5_72     rs11064    0.9099    53.21 1.381e-04
825829  rs760786796       22_2 rs760786796    0.9092    24.01 6.230e-05
746647   rs79979740      17_34  rs79979740    0.9088    33.53 8.694e-05
457606   rs35125576       8_85  rs35125576    0.9069    46.60 1.206e-04
464562     rs692503        9_5    rs692503    0.9062    47.68 1.233e-04
457053    rs4733814       8_84   rs4733814    0.9017    39.88 1.026e-04
321001    rs9391881       6_26   rs9391881    0.9015   520.45 1.339e-03
813816    rs3746372      20_37   rs3746372    0.9011    26.19 6.734e-05
602942    rs7968902      12_40   rs7968902    0.9009    48.61 1.250e-04
398310   rs60473539       7_62  rs60473539    0.8980    37.56 9.625e-05
921317   rs78065122       3_80  rs78065122    0.8954    36.17 9.240e-05
296486  rs144486602       5_78 rs144486602    0.8948    25.12 6.414e-05
497862    rs7045578       9_70   rs7045578    0.8913    27.17 6.911e-05
586594   rs12824533      12_11  rs12824533    0.8907    24.41 6.203e-05
457588   rs79584444       8_85  rs79584444    0.8902    49.33 1.253e-04
72570     rs9679004       2_16   rs9679004    0.8882    24.12 6.114e-05
780093   rs35639917       19_9  rs35639917    0.8874    55.35 1.401e-04
502035   rs10905634       10_7  rs10905634    0.8847    26.39 6.661e-05
367656   rs56703022        7_7  rs56703022    0.8837    28.94 7.296e-05
724897   rs12927351      16_39  rs12927351    0.8820    26.15 6.582e-05
421968   rs17151140       8_13  rs17151140    0.8813    29.13 7.325e-05
783175   rs34704748      19_15  rs34704748    0.8812    24.69 6.207e-05
5312      rs7546665       1_13   rs7546665    0.8804    26.76 6.721e-05
690873    rs2446407      15_21   rs2446407    0.8800    24.99 6.276e-05
690811    rs7169770      15_20   rs7169770    0.8758    28.06 7.012e-05
227861    rs7699743       4_69   rs7699743    0.8724    28.82 7.174e-05
207140     rs658080       4_31    rs658080    0.8715    26.22 6.519e-05
87324     rs7579497       2_47   rs7579497    0.8699    29.67 7.366e-05
782104   rs10420373      19_14  rs10420373    0.8687    57.96 1.437e-04
731657   rs57374020      16_53  rs57374020    0.8686    36.09 8.945e-05
828058  rs113934229       22_6 rs113934229    0.8681    26.68 6.608e-05
93325     rs1192820       2_59   rs1192820    0.8630    33.17 8.168e-05
853117   rs72683129       1_41  rs72683129    0.8626    70.63 1.738e-04
85826     rs1362478       2_44   rs1362478    0.8601    27.95 6.859e-05
77911    rs67584485       2_27  rs67584485    0.8596    36.97 9.068e-05
313944     rs201036        6_6    rs201036    0.8579    25.85 6.328e-05
814782    rs2823025       21_2   rs2823025    0.8536    26.60 6.478e-05
344433    rs9480643       6_71   rs9480643    0.8533    26.40 6.427e-05
396281          rs8       7_56         rs8    0.8503    30.18 7.322e-05
734864    rs9916791       17_7   rs9916791    0.8501    26.58 6.448e-05
20691   rs150467092       1_48 rs150467092    0.8498    25.93 6.288e-05
283260    rs7444298       5_52   rs7444298    0.8460    27.46 6.629e-05
375253   rs13229167       7_21  rs13229167    0.8420    40.04 9.620e-05
147697   rs11129979       3_31  rs11129979    0.8415    90.44 2.172e-04
808621    rs6095270      20_30   rs6095270    0.8399   152.74 3.661e-04
115481   rs36017642      2_109  rs36017642    0.8398    36.18 8.669e-05
807298   rs13043674      20_28  rs13043674    0.8377    26.13 6.246e-05
322383   rs34652732       6_29  rs34652732    0.8360    26.38 6.292e-05
840087  rs112682076        1_7 rs112682076    0.8349    35.20 8.385e-05
396277   rs17696150       7_56  rs17696150    0.8342   115.98 2.760e-04
948922  rs112655417        6_9 rs112655417    0.8337  6892.39 1.640e-02
604512    rs2137537      12_44   rs2137537    0.8337    24.96 5.937e-05
703724     rs899464      15_45    rs899464    0.8333    24.50 5.826e-05
26249      rs326664       1_59    rs326664    0.8332    25.93 6.165e-05
273793  rs149768957       5_32 rs149768957    0.8328    25.81 6.134e-05
644248    rs1330883      13_38   rs1330883    0.8325    27.49 6.531e-05
617064  rs117965634      12_67 rs117965634    0.8324    37.42 8.887e-05
603694    rs4913431      12_42   rs4913431    0.8308    29.79 7.063e-05
789513  rs559083563      19_29 rs559083563    0.8291    65.64 1.553e-04
521631   rs10997821      10_44  rs10997821    0.8282    32.30 7.634e-05
895772   rs75166367       2_97  rs75166367    0.8277    37.08 8.758e-05
161893   rs12493830       3_62  rs12493830    0.8255    30.87 7.272e-05
193168   rs66808687        4_2  rs66808687    0.8250    30.35 7.145e-05
695427   rs56906672      15_30  rs56906672    0.8234    26.56 6.239e-05
746953  rs148548662      17_34 rs148548662    0.8206    56.90 1.332e-04
38224    rs10753801       1_83  rs10753801    0.8206    24.58 5.756e-05
994761    rs3735485       7_33   rs3735485    0.8200   128.32 3.002e-04
510448    rs2807743      10_20   rs2807743    0.8175   122.29 2.853e-04
318422    rs6456418       6_15   rs6456418    0.8174    30.55 7.126e-05
368758   rs56195338       7_10  rs56195338    0.8154    43.70 1.017e-04
741296   rs12451746      17_21  rs12451746    0.8135    24.74 5.743e-05
825907   rs59667935       22_2  rs59667935    0.8133    25.65 5.952e-05
188346     rs720389      3_114    rs720389    0.8101    24.79 5.730e-05
464217   rs10733504        9_4  rs10733504    0.8099    28.00 6.471e-05
188464    rs6778003      3_114   rs6778003    0.8090    25.52 5.890e-05
955192  rs535876329       6_22 rs535876329    0.8048    35.81 8.223e-05
797951  rs117340493       20_7 rs117340493    0.8039    24.54 5.629e-05
274626   rs12658947       5_35  rs12658947    0.8005    39.89 9.111e-05
539260   rs17623606      10_78  rs17623606    0.8001    31.81 7.262e-05
               z
31705   -12.1006
58478   -14.3656
62820    10.3814
115498   11.9370
218483  -23.3384
221306    1.6324
377037   20.7223
396284  -10.9517
628523   11.9357
777917   -7.6886
825443    4.9695
825445    4.8177
868195  -14.0113
934104    2.4536
979576    1.7190
1147212 -17.9363
72545   -11.9143
9489    -15.8760
396257   -7.1423
321991   12.3107
958381   19.2276
868194    6.0106
437157  -10.8946
461756   11.1057
427615   -9.2035
376898    2.6504
979803  -28.1821
732773  -10.4026
613910    7.2629
211431    8.2732
974399   32.3917
301092   -6.8138
322031    8.3367
63028     7.0545
435508   -7.0571
576182    6.9446
115472    9.1085
716797   11.5382
461695   -7.0784
617055  -26.3817
980873   19.4379
111332   10.5684
584675   -6.2056
497983  -11.9575
806172    9.2187
320540   13.1014
379586    5.4645
8108      7.7223
353139   -2.5202
523143   -7.3565
777908   -1.1756
729549    7.8304
523156    6.8721
496491   -6.7645
379591   -3.9061
320502    8.5293
751350   -6.3725
314127    7.6921
221253  -12.5319
296841   -5.1644
770954   -5.7062
457576  -13.9906
766738    7.5188
969114  -11.0071
720077    6.6988
437188   -9.7350
609950   -9.0244
106994   -6.6131
506740    5.8663
316759   -8.1734
406898   -7.0822
320525   20.5510
406908    6.0194
545506    4.9613
442581   -5.7235
576191   10.2585
656688    5.3312
628525    8.8376
806136    6.5292
730241    5.0321
617243   -5.3274
826077   -5.6685
25283    -5.5066
324927   -4.9938
360634    7.2656
309233  -12.8046
301808   -5.2876
9492      9.8609
1030785  15.8381
584698    8.8972
211458   -9.2632
791644   -3.9295
471562   -9.6543
202261   -5.2962
743011   -5.2449
734895   -5.8528
530091    2.5648
423516   -5.0532
718211    5.1851
10181     6.4568
227127    5.4852
227815    5.8609
1054962   6.6894
397773   -5.9039
695299   -8.5754
678759    5.8530
125689   -6.1809
368103    7.1263
475470   -4.5565
206382    6.3327
483938   -7.2362
396361   -5.2273
2809      7.3965
77564     4.2466
82036     5.6673
697841   -5.1295
1090478   6.6352
753564    5.3438
798683   -5.4026
171334   -6.2026
546677   -5.7716
188427    4.6439
34996     5.7613
868196   -4.9802
154686   -5.4082
377034    7.7822
309184    5.1875
742719    5.8237
896157    6.9180
775807    4.7579
580061  -10.0269
748603    4.7536
7235     -6.2659
105084   -8.7371
115491    8.2415
666760   -4.7561
442541   -9.4469
742575    7.4417
597984   -5.5136
868188   -4.8708
134685   -4.7395
572215    6.2129
78782     5.2992
787395    5.1593
634076    4.6345
399732    4.8593
850036    4.3921
35287    -8.1097
658620   10.8893
655446   -4.9404
717874    5.2069
557710   -5.3299
1157394   6.9349
314121    5.5926
407931   -5.5257
619609   -5.3471
952042   -9.7257
456525    5.3060
58154     7.0545
729892   -5.3814
794200    4.5892
207362    7.4784
339574   -7.5075
535580   -5.0133
320571   -5.8011
731521    5.4841
620644    6.4063
48861    -5.3338
49375    10.2518
952603    8.5058
484266   -4.4269
464528   -6.5608
607240   -5.2670
217915   -8.0809
412146    4.9752
318103    4.1644
582018   -4.5946
779131   -8.0320
319081   -4.7844
598993    4.6105
422373    6.6410
530143   -4.4662
928994   -7.6381
318840    5.0209
711583    3.8732
738239   -8.3444
292988   -7.5808
825829    4.4313
746647   -5.7245
457606   -6.9790
464562    7.5243
457053    7.7217
321001   29.7491
813816   -4.8715
602942    6.8687
398310   -3.9742
921317   -6.1001
296486   -4.8858
497862    5.2746
586594    4.5310
457588   -6.2508
72570     3.3681
780093   -9.5115
502035    4.8594
367656    5.3596
724897    4.7348
421968    3.0103
783175    4.2712
5312      4.8663
690873    4.7005
690811   -2.9983
227861   -4.4658
207140   -4.4771
87324    -5.2861
782104   -9.2524
731657   -5.6078
828058   -5.3105
93325     5.5006
853117   12.7746
85826     4.9226
77911    -6.1157
313944    4.5511
814782    5.1986
344433    4.7105
396281    4.9715
734864    4.3527
20691     4.5431
283260   -4.8603
375253    6.5229
147697  -10.1402
808621    1.4297
115481   -1.8327
807298   -4.6724
322383    4.3281
840087   -6.3056
396277  -11.6557
948922   -0.3897
604512   -4.7285
703724   -4.5188
26249     4.8992
273793   -5.0365
644248   -4.5407
617064   -7.5514
603694   -5.3758
789513    8.2187
521631   -5.4996
895772   -6.3367
161893    5.2481
193168    5.1512
695427   -4.5684
746953    7.6171
38224    -4.3837
994761   11.7187
510448   11.5079
318422   -5.4925
368758   -6.4972
741296    4.5802
825907    5.0353
188346   -4.0308
464217   -4.1988
188464   -4.5603
955192    5.8186
797951   -3.8163
274626    5.9971
539260    5.9897

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        id.1 susie_pip   mu2       PVE      z
825445  rs13049893      21_24  rs13049893 1.000e+00 19430 5.544e-02  4.818
825443  rs13049759      21_24  rs13049759 1.000e+00 19341 5.519e-02  4.970
825430  rs13052701      21_24  rs13052701 0.000e+00 16370 0.000e+00  4.944
825433 rs147757092      21_24 rs147757092 0.000e+00 14934 0.000e+00  4.614
825476  rs11702800      21_24  rs11702800 0.000e+00 14349 0.000e+00 -5.560
825489   rs2268523      21_24   rs2268523 0.000e+00 14313 0.000e+00 -5.586
825486   rs9981445      21_24   rs9981445 0.000e+00 14077 0.000e+00 -5.570
825506   rs2839257      21_24   rs2839257 0.000e+00 13981 0.000e+00 -5.710
825470  rs11909986      21_24  rs11909986 0.000e+00 12579 0.000e+00  6.006
825424  rs35679325      21_24  rs35679325 0.000e+00 12250 0.000e+00 -5.090
825441   rs4819221      21_24   rs4819221 0.000e+00 12208 0.000e+00  5.060
979573   rs3869130       6_25   rs3869130 3.125e-01 12143 1.083e-02 14.055
979574   rs3869131       6_25   rs3869131 1.870e-01 12143 6.479e-03 14.047
979570   rs3899823       6_25   rs3899823 4.284e-01 12142 1.484e-02 14.063
979586  rs34259803       6_25  rs34259803 4.423e-02 12140 1.532e-03 14.034
979571   rs3869129       6_25   rs3869129 2.788e-02 12136 9.653e-04 14.056
825449   rs4818832      21_24   rs4818832 0.000e+00 12119 0.000e+00  5.082
825448  rs62226478      21_24  rs62226478 0.000e+00 12116 0.000e+00  5.087
979563  rs73404245       6_25  rs73404245 5.850e-08 12100 2.020e-09 13.998
825446  rs34586434      21_24  rs34586434 0.000e+00 12094 0.000e+00  5.094
979576 rs201369106       6_25 rs201369106 1.000e+00 12077 3.446e-02  1.719
979582   rs7769942       6_25   rs7769942 8.882e-16 11984 3.037e-17 14.605
979560 rs566631013       6_25 rs566631013 0.000e+00 11108 0.000e+00 12.820
979558 rs373478096       6_25 rs373478096 0.000e+00 11108 0.000e+00 12.820
979559 rs200256874       6_25 rs200256874 0.000e+00 11108 0.000e+00 12.820
825437   rs2032226      21_24   rs2032226 0.000e+00 10457 0.000e+00  5.361
825431   rs4535149      21_24   rs4535149 0.000e+00 10369 0.000e+00  5.360
979218   rs9501109       6_25   rs9501109 0.000e+00 10123 0.000e+00 16.607
825421   rs2001809      21_24   rs2001809 0.000e+00  9906 0.000e+00  3.733
979285  rs60539855       6_25  rs60539855 0.000e+00  9532 0.000e+00 16.465
979652   rs4458721       6_25   rs4458721 0.000e+00  9423 0.000e+00 16.419
979588  rs73404265       6_25  rs73404265 0.000e+00  9172 0.000e+00 13.695
979581   rs7769403       6_25   rs7769403 0.000e+00  9171 0.000e+00 13.693
825426   rs4819218      21_24   rs4819218 0.000e+00  8965 0.000e+00  4.926
825425   rs2280959      21_24   rs2280959 0.000e+00  8953 0.000e+00  4.934
825511   rs2073381      21_24   rs2073381 0.000e+00  8897 0.000e+00  4.936
979330 rs117813801       6_25 rs117813801 0.000e+00  8779 0.000e+00 13.870
979360 rs114921825       6_25 rs114921825 0.000e+00  8779 0.000e+00 13.705
979331 rs143741838       6_25 rs143741838 0.000e+00  8779 0.000e+00 13.871
979355   rs4090415       6_25   rs4090415 0.000e+00  8774 0.000e+00 13.768
979353   rs4090417       6_25   rs4090417 0.000e+00  8773 0.000e+00 13.767
979354   rs4090416       6_25   rs4090416 0.000e+00  8773 0.000e+00 13.767
979351   rs9501116       6_25   rs9501116 0.000e+00  8773 0.000e+00 13.764
979350   rs9501115       6_25   rs9501115 0.000e+00  8772 0.000e+00 13.765
979555  rs28575156       6_25  rs28575156 0.000e+00  8768 0.000e+00 13.707
979388   rs2394999       6_25   rs2394999 0.000e+00  8765 0.000e+00 13.725
979382   rs2894212       6_25   rs2894212 0.000e+00  8765 0.000e+00 13.727
979384   rs4631325       6_25   rs4631325 0.000e+00  8765 0.000e+00 13.727
979387   rs2394998       6_25   rs2394998 0.000e+00  8765 0.000e+00 13.725
979380  rs80339222       6_25  rs80339222 0.000e+00  8765 0.000e+00 13.726

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        id.1 susie_pip     mu2       PVE        z
825445   rs13049893      21_24  rs13049893   1.00000 19430.2 0.0554404   4.8177
825443   rs13049759      21_24  rs13049759   1.00000 19341.2 0.0551865   4.9695
979576  rs201369106       6_25 rs201369106   1.00000 12076.7 0.0344586   1.7190
948922  rs112655417        6_9 rs112655417   0.83369  6892.4 0.0163954  -0.3897
979570    rs3899823       6_25   rs3899823   0.42840 12142.4 0.0148423  14.0629
948881     rs470863        6_9    rs470863   0.56473  6885.3 0.0110945  -0.4829
979573    rs3869130       6_25   rs3869130   0.31250 12143.2 0.0108276  14.0552
948894     rs470562        6_9    rs470562   0.41950  6885.7 0.0082420  -0.4744
979574    rs3869131       6_25   rs3869131   0.18699 12143.2 0.0064790  14.0471
974399    rs2524079       6_25   rs2524079   1.00000  2259.5 0.0064472  32.3917
934104  rs200599211       5_79 rs200599211   1.00000  1818.8 0.0051897   2.4536
980873    rs2229094       6_25   rs2229094   0.99999  1485.7 0.0042392  19.4379
979803    rs9267123       6_25   rs9267123   1.00000   869.1 0.0024797 -28.1821
948948  rs112850802        6_9 rs112850802   0.12491  6876.9 0.0024510  -0.3953
221306  rs529050451       4_56 rs529050451   1.00000   708.6 0.0020219   1.6324
617055     rs653178      12_67    rs653178   0.99999   573.8 0.0016371 -26.3817
979586   rs34259803       6_25  rs34259803   0.04423 12140.2 0.0015322  14.0343
218483    rs1371794       4_51   rs1371794   1.00000   476.0 0.0013583 -23.3384
321001    rs9391881       6_26   rs9391881   0.90152   520.4 0.0013388  29.7491
377037   rs56388170       7_24  rs56388170   1.00000   369.0 0.0010530  20.7223
979571    rs3869129       6_25   rs3869129   0.02788 12135.9 0.0009653  14.0556
221253    rs6814526       4_56   rs6814526   0.99979   309.1 0.0008818 -12.5319
1147212      rs4760      19_30      rs4760   1.00000   307.3 0.0008767 -17.9363
221309    rs9654217       4_56   rs9654217   0.42939   712.0 0.0008723   7.1517
221310    rs9654218       4_56   rs9654218   0.42509   712.0 0.0008636   7.1513
320525    rs2736155       6_26   rs2736155   0.99854   279.5 0.0007964  20.5510
437157    rs4738814       8_46   rs4738814   1.00000   235.4 0.0006717 -10.8946
969543    rs1264349       6_24   rs1264349   0.45458   502.0 0.0006511 -24.7873
958381    rs1233380       6_23   rs1233380   1.00000   223.4 0.0006376  19.2276
320477   rs67040724       6_21  rs67040724   0.71988   307.4 0.0006315 -18.4527
777917   rs12461480       19_4  rs12461480   1.00000   215.4 0.0006145  -7.6886
9489      rs3917932       1_22   rs3917932   1.00000   209.9 0.0005990 -15.8760
934118   rs13361914       5_79  rs13361914   0.10966  1809.9 0.0005663  -1.7542
1030785     rs14408       11_1     rs14408   0.99545   194.5 0.0005525  15.8381
934125   rs77753417       5_79  rs77753417   0.10675  1809.9 0.0005513  -1.7544
628523   rs79490353       13_7  rs79490353   1.00000   192.4 0.0005488  11.9357
321991   rs41258084       6_27  rs41258084   1.00000   189.9 0.0005419  12.3107
58478    rs10803164      1_122  rs10803164   1.00000   186.8 0.0005331 -14.3656
353114   rs56293029       6_89  rs56293029   0.60434   305.0 0.0005260 -16.9971
934121  rs113694337       5_79 rs113694337   0.10124  1809.8 0.0005228  -1.7519
509026  rs112955547      10_18 rs112955547   0.47367   385.0 0.0005203 -18.4434
969114    rs3131063       6_24   rs3131063   0.99952   180.9 0.0005158 -11.0071
868195   rs34599082       1_78  rs34599082   1.00000   177.7 0.0005070 -14.0113
321920    rs9276625       6_27   rs9276625   0.54185   327.5 0.0005064 -20.9363
958798    rs3131894       6_23   rs3131894   0.55281   314.4 0.0004960 -23.1028
320571  rs115487693       6_26 rs115487693   0.93719   182.6 0.0004882  -5.8011
948952   rs72819781        6_9  rs72819781   0.02476  6862.6 0.0004848  -0.4151
777908    rs2041128       19_4   rs2041128   0.99993   163.6 0.0004668  -1.1756
320540    rs1266074       6_26   rs1266074   0.99997   160.6 0.0004581  13.1014
963740    rs9260620       6_24   rs9260620   0.56272   276.7 0.0004442 -21.7153

SNPs with largest z scores

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

Version Author Date
684d806 sq-96 2023-01-26
#SNPs with 50 largest z scores
head(ctwas_snp_res[order(-abs(ctwas_snp_res$z)),report_cols_snps],50)
                 id region_tag        id.1 susie_pip   mu2       PVE      z
1108383   rs8078723      17_23   rs8078723 2.011e-03 608.4 3.491e-06  37.33
1108420    rs709592      17_23    rs709592 2.349e-03 609.6 4.085e-06  37.32
1108421    rs709591      17_23    rs709591 1.994e-03 608.9 3.465e-06  37.31
1108375  rs55771023      17_23  rs55771023 1.504e-03 607.4 2.607e-06  37.30
1108374  rs55736351      17_23  rs55736351 1.422e-03 607.2 2.463e-06  37.30
1108339   rs4795414      17_23   rs4795414 1.028e-03 605.6 1.776e-06  37.30
1108340   rs4795415      17_23   rs4795415 1.026e-03 605.6 1.774e-06  37.30
1108341   rs4795416      17_23   rs4795416 1.021e-03 605.5 1.765e-06  37.30
1108350   rs8065519      17_23   rs8065519 1.019e-03 605.6 1.760e-06  37.30
1108335  rs56922390      17_23  rs56922390 9.628e-04 605.3 1.663e-06  37.29
1108361  rs12602172      17_23  rs12602172 9.388e-04 605.5 1.622e-06  37.29
1108334   rs4794822      17_23   rs4794822 8.848e-04 605.1 1.528e-06  37.29
1108369  rs55846942      17_23  rs55846942 9.324e-04 605.5 1.611e-06  37.29
1108359  rs12600856      17_23  rs12600856 9.182e-04 605.4 1.586e-06  37.29
1108380   rs4795419      17_23   rs4795419 9.409e-04 605.6 1.626e-06  37.29
1108381   rs4794823      17_23   rs4794823 8.888e-04 605.4 1.535e-06  37.29
1108353   rs8070454      17_23   rs8070454 8.040e-04 604.9 1.388e-06  37.29
1108372   rs4795418      17_23   rs4795418 8.301e-04 605.2 1.433e-06  37.29
1108355   rs6503530      17_23   rs6503530 7.779e-04 604.8 1.342e-06  37.28
1108376   rs7221894      17_23   rs7221894 7.095e-04 604.6 1.224e-06  37.28
1108417   rs2227336      17_23   rs2227336 6.848e-04 604.9 1.182e-06  37.27
1108404   rs2227322      17_23   rs2227322 6.025e-04 604.4 1.039e-06  37.27
1108415   rs1042658      17_23   rs1042658 6.174e-04 604.5 1.065e-06  37.27
1108425  rs11871747      17_23  rs11871747 5.111e-04 605.3 8.826e-07  37.26
1108393   rs7208815      17_23   rs7208815 5.882e-04 604.3 1.014e-06  37.26
1108386   rs4795420      17_23   rs4795420 4.990e-04 603.6 8.594e-07  37.26
1108385  rs62065177      17_23  rs62065177 4.922e-04 603.5 8.477e-07  37.26
1108395   rs7214085      17_23   rs7214085 4.746e-04 603.4 8.172e-07  37.26
1108390  rs57065891      17_23  rs57065891 4.714e-04 603.4 8.117e-07  37.26
1108398  rs59925331      17_23  rs59925331 4.691e-04 603.4 8.076e-07  37.26
1108399   rs2227315      17_23   rs2227315 4.407e-04 603.2 7.584e-07  37.25
1108326      rs7021      17_23      rs7021 3.290e-04 601.4 5.646e-07  37.24
1108317   rs4795412      17_23   rs4795412 2.895e-04 600.8 4.963e-07  37.23
1108330   rs8081692      17_23   rs8081692 2.921e-04 601.0 5.010e-07  37.23
1108293  rs57968500      17_23  rs57968500 2.284e-04 599.5 3.907e-07  37.22
1108432   rs4794824      17_23   rs4794824 1.008e-04 600.6 1.727e-07  37.13
1108430   rs3213762      17_23   rs3213762 2.695e-05 595.3 4.578e-08  37.07
1108356 rs111848559      17_23 rs111848559 5.049e-05 596.4 8.592e-08  37.06
1108447   rs6503533      17_23   rs6503533 1.088e-05 605.6 1.879e-08 -36.96
1108316   rs3826331      17_23   rs3826331 3.769e-09 580.5 6.242e-12 -36.93
1108418   rs1045929      17_23   rs1045929 1.595e-06 586.9 2.671e-09  36.89
1108304  rs60666652      17_23  rs60666652 2.155e-07 582.8 3.583e-10  36.72
1108303  rs60082402      17_23  rs60082402 2.021e-07 582.6 3.360e-10  36.72
1108389  rs60005225      17_23  rs60005225 4.537e-08 577.5 7.476e-11  36.67
1108347  rs12941811      17_23  rs12941811 7.362e-12 582.0 1.222e-14 -36.55
1108321   rs8070444      17_23   rs8070444 3.087e-11 578.5 5.095e-14 -35.99
1108289  rs12450688      17_23  rs12450688 3.433e-11 581.0 5.691e-14 -35.98
1108272   rs2305482      17_23   rs2305482 4.329e-11 583.2 7.204e-14 -35.98
1108322   rs8071037      17_23   rs8071037 2.883e-11 576.9 4.746e-14 -35.97
1108292   rs9915252      17_23   rs9915252 3.184e-11 579.3 5.263e-14 -35.96

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