Last updated: 2023-01-23

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Weight QC

[1] 11502
[1] 3159

  1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19  20 
303 212 161 125 140 200 169 111 120 118 187 178  52 100 102 172 194  47 238  91 
 21  22 
 45  94 
[1] 1

Load ctwas results

Check convergence of parameters

    gene      snp 
0.001823 0.001739 
 gene   snp 
11.07 52.98 
[1] 1.048
[1] 343621
[1]    3159 8696600
     gene       snp 
0.0001855 2.3315048 
[1] 2.332
     gene 
7.954e-05 

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
4433      PSRC1       1_67    1.0000 1676.75 4.880e-03 -41.687        1
11327       HPR      16_38    1.0000  452.14 1.316e-03 -16.590        1
NA.365     <NA>      1_121    0.9997  204.92 5.962e-04 -15.108        1
4315    ANGPTL3       1_39    0.9964  251.54 7.294e-04  16.132        1
8523       TNKS       8_12    0.9955   77.42 2.243e-04  10.918        1
5988      FADS1      11_34    0.9952  156.60 4.536e-04  12.587        1
1597       PLTP      20_28    0.9920   61.78 1.784e-04  -5.732        1
10708    NYNRIN       14_3    0.9917   58.17 1.679e-04   7.679        1
9365       GAS6      13_62    0.9908   71.37 2.058e-04  -8.924        1
2092        SP4       7_19    0.9807  103.07 2.941e-04  10.693        1
6090    CSNK1G3       5_75    0.9800   84.95 2.423e-04   9.116        1
6774       PKN3       9_66    0.9791   48.00 1.368e-04  -6.621        1
11257    CYP2A6      19_28    0.9757   32.76 9.303e-05   5.407        1
9251     ZNF329      19_39    0.9695  107.38 3.030e-04  10.059        1
2454    ST3GAL4      11_77    0.9508   82.25 2.276e-04  11.943        1
9046    KLHDC7A       1_13    0.8879   21.57 5.573e-05   4.124        1
6615      TMED4       7_32    0.8801   55.44 1.420e-04   9.455        1
3720     INSIG2       2_69    0.8789   45.34 1.160e-04  -6.998        1
9054    SPTY2D1      11_13    0.8656   33.81 8.518e-05  -5.557        1
6097       ALLC        2_2    0.8554   28.16 7.009e-05   4.919        1
1309       FMO2       1_84    0.8521   27.55 6.832e-05   4.821        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 6380.59 0.000e+00  -6.593        1
10399       LPA      6_104 0.000e+00 1997.74 0.000e+00   8.120        1
4433      PSRC1       1_67 1.000e+00 1676.75 4.880e-03 -41.687        1
11327       HPR      16_38 1.000e+00  452.14 1.316e-03 -16.590        1
NA.122     <NA>      6_104 0.000e+00  353.45 0.000e+00  -8.475        1
4315    ANGPTL3       1_39 9.964e-01  251.54 7.294e-04  16.132        1
NA.159     <NA>       8_83 4.677e-03  243.37 3.313e-06  14.404        1
NA.365     <NA>      1_121 9.997e-01  204.92 5.962e-04 -15.108        1
11471    PKD1L3      16_38 2.693e-06  176.63 1.384e-09   4.999        1
5988      FADS1      11_34 9.952e-01  156.60 4.536e-04  12.587        1
9251     ZNF329      19_39 9.695e-01  107.38 3.030e-04  10.059        1
2092        SP4       7_19 9.807e-01  103.07 2.941e-04  10.693        1
781         PVR      19_31 0.000e+00  102.05 0.000e+00  -3.544        1
9910       RHCE       1_18 4.153e-01  101.60 1.228e-04  10.264        1
4047    NECTIN2      19_31 0.000e+00  100.08 0.000e+00   5.825        1
9718   CEACAM19      19_31 0.000e+00   99.39 0.000e+00 -10.909        1
9428    TMEM50A       1_18 8.126e-02   98.23 2.323e-05  10.082        1
2309      KPNB1      17_27 3.386e-01   98.00 9.656e-05  -9.909        1
9438    EMILIN3      20_25 2.540e-02   93.34 6.901e-06   9.502        1
6090    CSNK1G3       5_75 9.800e-01   84.95 2.423e-04   9.116        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
4433      PSRC1       1_67    1.0000 1676.75 4.880e-03 -41.687        1
11327       HPR      16_38    1.0000  452.14 1.316e-03 -16.590        1
4315    ANGPTL3       1_39    0.9964  251.54 7.294e-04  16.132        1
NA.365     <NA>      1_121    0.9997  204.92 5.962e-04 -15.108        1
5988      FADS1      11_34    0.9952  156.60 4.536e-04  12.587        1
9251     ZNF329      19_39    0.9695  107.38 3.030e-04  10.059        1
2092        SP4       7_19    0.9807  103.07 2.941e-04  10.693        1
6090    CSNK1G3       5_75    0.9800   84.95 2.423e-04   9.116        1
2454    ST3GAL4      11_77    0.9508   82.25 2.276e-04  11.943        1
8523       TNKS       8_12    0.9955   77.42 2.243e-04  10.918        1
9365       GAS6      13_62    0.9908   71.37 2.058e-04  -8.924        1
1597       PLTP      20_28    0.9920   61.78 1.784e-04  -5.732        1
10708    NYNRIN       14_3    0.9917   58.17 1.679e-04   7.679        1
6615      TMED4       7_32    0.8801   55.44 1.420e-04   9.455        1
6774       PKN3       9_66    0.9791   48.00 1.368e-04  -6.621        1
9910       RHCE       1_18    0.4153  101.60 1.228e-04  10.264        1
3720     INSIG2       2_69    0.8789   45.34 1.160e-04  -6.998        1
2309      KPNB1      17_27    0.3386   98.00 9.656e-05  -9.909        1
11257    CYP2A6      19_28    0.9757   32.76 9.303e-05   5.407        1
9054    SPTY2D1      11_13    0.8656   33.81 8.518e-05  -5.557        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
4433      PSRC1       1_67  1.000000 1676.75 4.880e-03 -41.687        1
11327       HPR      16_38  1.000000  452.14 1.316e-03 -16.590        1
4315    ANGPTL3       1_39  0.996428  251.54 7.294e-04  16.132        1
NA.365     <NA>      1_121  0.999665  204.92 5.962e-04 -15.108        1
NA.159     <NA>       8_83  0.004677  243.37 3.313e-06  14.404        1
5988      FADS1      11_34  0.995191  156.60 4.536e-04  12.587        1
2454    ST3GAL4      11_77  0.950820   82.25 2.276e-04  11.943        1
8523       TNKS       8_12  0.995525   77.42 2.243e-04  10.918        1
9718   CEACAM19      19_31  0.000000   99.39 0.000e+00 -10.909        1
2092        SP4       7_19  0.980670  103.07 2.941e-04  10.693        1
9910       RHCE       1_18  0.415254  101.60 1.228e-04  10.264        1
9428    TMEM50A       1_18  0.081259   98.23 2.323e-05  10.082        1
9251     ZNF329      19_39  0.969485  107.38 3.030e-04  10.059        1
2309      KPNB1      17_27  0.338600   98.00 9.656e-05  -9.909        1
9438    EMILIN3      20_25  0.025404   93.34 6.901e-06   9.502        1
6615      TMED4       7_32  0.880091   55.44 1.420e-04   9.455        1
6090    CSNK1G3       5_75  0.980012   84.95 2.423e-04   9.116        1
9365       GAS6      13_62  0.990760   71.37 2.058e-04  -8.924        1
11016     APOC2      19_31  0.000000   53.52 0.000e+00  -8.870        1
11372     APOC4      19_31  0.000000   51.50 0.000e+00   8.735        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$z) > sig_thresh)
[1] 101
#proportion of significant z scores
mean(abs(ctwas_gene_res$z) > sig_thresh)
[1] 0.03197
#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
4433      PSRC1       1_67  1.000000 1676.75 4.880e-03 -41.687        1
11327       HPR      16_38  1.000000  452.14 1.316e-03 -16.590        1
4315    ANGPTL3       1_39  0.996428  251.54 7.294e-04  16.132        1
NA.365     <NA>      1_121  0.999665  204.92 5.962e-04 -15.108        1
NA.159     <NA>       8_83  0.004677  243.37 3.313e-06  14.404        1
5988      FADS1      11_34  0.995191  156.60 4.536e-04  12.587        1
2454    ST3GAL4      11_77  0.950820   82.25 2.276e-04  11.943        1
8523       TNKS       8_12  0.995525   77.42 2.243e-04  10.918        1
9718   CEACAM19      19_31  0.000000   99.39 0.000e+00 -10.909        1
2092        SP4       7_19  0.980670  103.07 2.941e-04  10.693        1
9910       RHCE       1_18  0.415254  101.60 1.228e-04  10.264        1
9428    TMEM50A       1_18  0.081259   98.23 2.323e-05  10.082        1
9251     ZNF329      19_39  0.969485  107.38 3.030e-04  10.059        1
2309      KPNB1      17_27  0.338600   98.00 9.656e-05  -9.909        1
9438    EMILIN3      20_25  0.025404   93.34 6.901e-06   9.502        1
6615      TMED4       7_32  0.880091   55.44 1.420e-04   9.455        1
6090    CSNK1G3       5_75  0.980012   84.95 2.423e-04   9.116        1
9365       GAS6      13_62  0.990760   71.37 2.058e-04  -8.924        1
11016     APOC2      19_31  0.000000   53.52 0.000e+00  -8.870        1
11372     APOC4      19_31  0.000000   51.50 0.000e+00   8.735        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
14831     rs2495502       1_34    1.0000   300.73 8.752e-04   6.2922
68843     rs1042034       2_13    1.0000   237.63 6.915e-04  16.5730
68849      rs934197       2_13    1.0000   414.98 1.208e-03  33.0609
70579      rs780093       2_16    1.0000   167.21 4.866e-04 -14.1426
368612   rs12208357      6_103    1.0000   244.15 7.105e-04  12.2823
368715   rs60425481      6_104    1.0000 34617.58 1.007e-01  -7.1125
761755  rs113408695      17_39    1.0000   146.62 4.267e-04  12.7688
795613   rs73013176       19_9    1.0000   240.92 7.011e-04 -16.2327
805450   rs62117204      19_31    1.0000   825.83 2.403e-03 -44.6722
805468  rs111794050      19_31    1.0000   771.38 2.245e-03 -33.5996
805501     rs814573      19_31    1.0000  2231.68 6.495e-03  55.5379
805503  rs113345881      19_31    1.0000   781.13 2.273e-03 -34.3186
805506   rs12721109      19_31    1.0000  1355.57 3.945e-03 -46.3258
798144    rs3794991      19_15    1.0000   435.64 1.268e-03 -21.4921
761781    rs8070232      17_39    1.0000   152.14 4.428e-04  -8.0915
816677   rs34507316      20_13    1.0000    80.71 2.349e-04  -6.8147
68794    rs11679386       2_12    1.0000   132.05 3.843e-04  11.9094
68929     rs1848922       2_13    1.0000   231.66 6.742e-04  25.4123
68852      rs548145       2_13    1.0000   664.99 1.935e-03  33.0860
496315    rs2437818       9_53    1.0000    69.92 2.035e-04   6.3340
1015362   rs1800961      20_28    1.0000    72.56 2.112e-04  -8.8970
504532  rs115478735       9_70    1.0000   307.40 8.946e-04  19.0118
805841  rs150262789      19_32    1.0000    77.88 2.266e-04 -10.8985
760839    rs1801689      17_38    1.0000    80.97 2.356e-04   9.3964
805164   rs73036721      19_30    1.0000    58.65 1.707e-04  -7.7879
443063    rs4738679       8_45    1.0000   108.15 3.147e-04 -11.6999
274809    rs1499279       5_30    1.0000    62.03 1.805e-04  -8.3746
76644    rs72800939       2_28    1.0000    55.98 1.629e-04  -7.8457
795651  rs137992968       19_9    1.0000   114.51 3.333e-04 -10.7526
14842    rs10888896       1_34    1.0000   134.32 3.909e-04  11.8938
7646     rs79598313       1_18    1.0000    46.89 1.365e-04   7.0246
462724   rs13252684       8_83    1.0000   227.38 6.617e-04  11.9644
441668  rs140753685       8_42    1.0000    55.16 1.605e-04   7.7992
805209   rs62115478      19_30    1.0000   183.16 5.330e-04 -14.3262
52998     rs2807848      1_112    1.0000    54.88 1.597e-04  -7.8828
14801    rs11580527       1_34    1.0000    88.52 2.576e-04 -11.1672
14849      rs471705       1_34    1.0000   210.38 6.122e-04  16.2630
350049    rs9496567       6_67    1.0000    38.86 1.131e-04  -6.3402
319854   rs11376017       6_13    0.9999    65.40 1.903e-04  -8.5079
795677    rs4804149      19_10    0.9999    46.15 1.343e-04   6.5194
816676    rs6075251      20_13    0.9998    53.98 1.571e-04  -2.3298
798175  rs113619686      19_15    0.9998    56.13 1.633e-04   0.5939
76508   rs139029940       2_27    0.9997    39.11 1.138e-04   6.8150
703812    rs2070895      15_26    0.9996    58.63 1.706e-04   7.7347
368803  rs374071816      6_104    0.9996  6415.76 1.866e-02  16.2541
795642    rs1569372       19_9    0.9993   278.34 8.095e-04  10.0055
542886   rs17875416      10_71    0.9993    37.72 1.097e-04  -6.2663
795637    rs3745677       19_9    0.9993    90.85 2.642e-04   9.3358
795730     rs322144      19_10    0.9992    56.74 1.650e-04   3.9466
323940     rs454182       6_22    0.9992    35.39 1.029e-04   4.7791
609330    rs7397189      12_36    0.9991    34.12 9.920e-05  -5.7710
496288    rs2297400       9_53    0.9989    40.92 1.190e-04   6.6057
795634  rs147985405       19_9    0.9986  2286.17 6.644e-03 -48.9352
281261    rs7701166       5_44    0.9986    33.45 9.719e-05  -2.4848
797784    rs2302209      19_14    0.9981    42.79 1.243e-04   6.6360
431395    rs1495743       8_20    0.9978    40.73 1.183e-04  -6.5160
740565    rs2255451      16_48    0.9959    38.08 1.104e-04  -6.3628
585721    rs3135506      11_70    0.9956   147.38 4.270e-04  12.3730
443031   rs56386732       8_45    0.9955    34.46 9.983e-05  -7.0123
585726   rs75542613      11_70    0.9954    35.61 1.032e-04  -6.5344
821630   rs76981217      20_24    0.9953    35.23 1.020e-04   7.6925
324377    rs3130253       6_23    0.9942    29.66 8.583e-05   5.6415
613696  rs148481241      12_44    0.9929    27.35 7.902e-05   5.0955
625914     rs653178      12_67    0.9924    92.80 2.680e-04  11.0501
281202   rs10062361       5_44    0.9869   202.05 5.803e-04  20.3206
806761     rs838145      19_33    0.9856    97.91 2.809e-04 -11.8738
735238    rs4396539      16_37    0.9854    27.36 7.847e-05  -5.2329
137892     rs709149        3_9    0.9851    35.61 1.021e-04  -6.7820
325162   rs28780090       6_24    0.9829    49.14 1.406e-04   6.8714
404191    rs3197597       7_61    0.9818    29.19 8.339e-05  -5.0452
630003   rs11057830      12_76    0.9809    25.68 7.330e-05   4.9296
325185   rs62407548       6_24    0.9802    63.62 1.815e-04   8.2573
144902    rs9834932       3_24    0.9801    65.63 1.872e-04  -8.4816
821581    rs6029132      20_24    0.9795    39.13 1.115e-04  -6.7625
821634   rs73124945      20_24    0.9793    32.10 9.150e-05  -7.7754
388423  rs141379002       7_33    0.9720    25.45 7.200e-05   4.8970
470776    rs7024888        9_3    0.9695    25.42 7.173e-05  -5.0558
462713   rs79658059       8_83    0.9690   269.87 7.611e-04 -16.0220
244616  rs114756490      4_100    0.9690    26.06 7.349e-05   4.9889
805824   rs34942359      19_32    0.9676    62.00 1.746e-04  -7.0096
829635   rs62219001       21_2    0.9626    25.96 7.273e-05  -4.9484
221887    rs1458038       4_54    0.9600    52.32 1.462e-04  -7.4179
478640    rs1556516       9_16    0.9557    72.76 2.024e-04  -8.9921
594353   rs11048034       12_9    0.9540    35.50 9.856e-05   6.1337
764914    rs4969183      17_44    0.9522    48.50 1.344e-04   7.1693
628868    rs1169300      12_74    0.9474    67.72 1.867e-04   8.6855
323401   rs75080831       6_19    0.9439    56.44 1.550e-04  -7.9067
624007    rs1196760      12_63    0.9412    25.69 7.036e-05  -4.8667
324348   rs28986304       6_23    0.9319    41.73 1.132e-04   7.3825
76524     rs4076834       2_27    0.9314   425.49 1.153e-03 -20.1086
352785   rs12199109       6_73    0.9272    24.50 6.609e-05   4.8570
569350    rs6591179      11_36    0.9265    24.78 6.683e-05   4.8933
193512    rs5855544      3_120    0.9264    23.69 6.387e-05  -4.5937
76521    rs13430143       2_27    0.9231    76.76 2.062e-04  -3.3445
68846    rs78610189       2_13    0.9181    59.17 1.581e-04  -8.3855
368606    rs9456502      6_103    0.9140    33.08 8.798e-05   5.9640
427072  rs117037226       8_11    0.9072    23.62 6.237e-05   4.1922
805741  rs377297589      19_32    0.9063    50.46 1.331e-04  -6.7865
14832     rs1887552       1_34    0.9063   344.07 9.075e-04  -9.8686
751298  rs117859452      17_17    0.9031    24.14 6.345e-05  -3.8517
836876    rs2835302      21_16    0.9017    25.15 6.598e-05  -4.6537
703811  rs139823028      15_26    0.8994    23.59 6.175e-05   3.9898
195299   rs36205397        4_4    0.8993    38.35 1.004e-04   6.1594
169895     rs189174       3_74    0.8954    43.56 1.135e-04   6.7678
731346     rs821840      16_30    0.8951   163.02 4.247e-04 -13.4753
509482   rs10905277       10_8    0.8941    27.80 7.234e-05   5.1258
812322   rs74273659       20_5    0.8931    24.47 6.360e-05   4.6468
197524    rs2002574       4_10    0.8920    24.29 6.304e-05  -4.5583
542597   rs12244851      10_70    0.8902    36.36 9.420e-05  -4.8831
795718     rs322125      19_10    0.8873   101.66 2.625e-04  -7.4704
751207    rs3032928      17_17    0.8835    33.72 8.669e-05   6.1119
496308    rs2777788       9_53    0.8783    57.78 1.477e-04  -5.7370
581990  rs201912654      11_59    0.8714    39.91 1.012e-04  -6.3056
825133   rs10641149      20_32    0.8687    26.93 6.807e-05   5.0758
638890    rs1012130      13_10    0.8681    38.76 9.792e-05  -2.7810
848964  rs145678077      22_17    0.8565    24.69 6.154e-05  -4.8686
119989    rs7569317      2_120    0.8546    44.04 1.095e-04   7.9007
68646     rs6531234       2_12    0.8543    42.09 1.046e-04  -7.1708
795687   rs58495388      19_10    0.8501    33.71 8.338e-05   5.5313
486626   rs11144506       9_35    0.8486    26.90 6.644e-05   5.0427
358988    rs9321207       6_86    0.8475    30.33 7.481e-05   5.4016
821599    rs6102034      20_24    0.8443    96.35 2.367e-04 -11.1900
281225    rs3843482       5_44    0.8372   395.85 9.645e-04  25.0344
820375   rs11167269      20_21    0.8326    56.80 1.376e-04  -7.7950
756426    rs4793601      17_28    0.8268    30.55 7.352e-05  -6.2095
816657   rs78348000      20_13    0.8209    30.02 7.171e-05   5.2206
536776   rs10882161      10_59    0.8165    29.78 7.076e-05  -5.4756
761766    rs9303012      17_39    0.8164   144.47 3.432e-04   2.2591
638882    rs1799955      13_10    0.8149    69.86 1.657e-04  -6.6936
793033   rs12459030       19_4    0.8133    24.48 5.794e-05  -4.3721
722803   rs35782593      16_12    0.8132    24.15 5.716e-05  -4.3189

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
368711   rs3106169      6_104 6.210e-01 34666 6.265e-02 11.139
368712   rs3127598      6_104 4.710e-01 34665 4.752e-02 11.135
368720   rs3106167      6_104 4.787e-01 34665 4.829e-02 11.136
368704  rs11755965      6_104 1.257e-01 34655 1.268e-02 11.140
368715  rs60425481      6_104 1.000e+00 34618 1.007e-01 -7.113
368695  rs12194962      6_104 4.484e-07 34582 4.512e-08 11.106
368713   rs3127597      6_104 7.406e-08 34560 7.448e-09 11.145
368674   rs3119311      6_104 0.000e+00 25050 0.000e+00  8.031
368668   rs3127579      6_104 0.000e+00 18252 0.000e+00  7.568
368662  rs10945658      6_104 0.000e+00 15988 0.000e+00  8.309
368657   rs3103352      6_104 0.000e+00 15952 0.000e+00  8.522
368661   rs3119308      6_104 0.000e+00 15949 0.000e+00  8.274
368653   rs3101821      6_104 0.000e+00 15896 0.000e+00  8.528
368659  rs12205178      6_104 0.000e+00 15859 0.000e+00  8.297
368651 rs148015788      6_104 0.000e+00 15660 0.000e+00  8.351
368762   rs3124784      6_104 0.000e+00 13154 0.000e+00  9.680
368763   rs3127596      6_104 0.000e+00 11943 0.000e+00  9.556
368756   rs3127599      6_104 0.000e+00 11880 0.000e+00  9.259
368726   rs2481030      6_104 0.000e+00 11348 0.000e+00  4.811
368691   rs2504949      6_104 0.000e+00  9336 0.000e+00  2.937
368744    rs388170      6_104 0.000e+00  8646 0.000e+00  3.833
368666    rs316013      6_104 0.000e+00  8286 0.000e+00 -3.002
368667    rs316012      6_104 0.000e+00  8187 0.000e+00 -3.074
368747   rs9355288      6_104 0.000e+00  8030 0.000e+00  6.319
368655    rs610206      6_104 0.000e+00  7566 0.000e+00 -2.944
368656    rs595374      6_104 0.000e+00  7551 0.000e+00 -2.921
368663    rs315995      6_104 0.000e+00  7369 0.000e+00 -3.207
368660    rs543435      6_104 0.000e+00  7342 0.000e+00 -3.250
368709    rs452867      6_104 0.000e+00  6963 0.000e+00 -7.124
368718    rs367334      6_104 0.000e+00  6958 0.000e+00 -7.106
368706    rs589931      6_104 0.000e+00  6957 0.000e+00 -7.116
368707    rs600584      6_104 0.000e+00  6957 0.000e+00 -7.113
368708    rs434953      6_104 0.000e+00  6957 0.000e+00 -7.111
368714    rs380498      6_104 0.000e+00  6957 0.000e+00 -7.115
368682   rs3119312      6_104 0.000e+00  6639 0.000e+00  3.771
368803 rs374071816      6_104 9.996e-01  6416 1.866e-02 16.254
368741   rs2872317      6_104 0.000e+00  6123 0.000e+00  6.746
368738   rs2313453      6_104 0.000e+00  6118 0.000e+00  6.718
368808   rs4252185      6_104 4.487e-04  5922 7.732e-06 15.878
368729 rs146184004      6_104 0.000e+00  5824 0.000e+00  6.534
368732    rs624319      6_104 0.000e+00  5759 0.000e+00 -6.291
368731    rs637614      6_104 0.000e+00  5752 0.000e+00 -6.362
368733    rs486339      6_104 0.000e+00  5712 0.000e+00 -6.311
368678    rs316036      6_104 0.000e+00  5610 0.000e+00 -7.009
368730    rs555754      6_104 0.000e+00  5572 0.000e+00 -6.593
368809  rs12212146      6_104 0.000e+00  4422 0.000e+00 -2.410
368676    rs582280      6_104 0.000e+00  4291 0.000e+00  2.635
368675    rs497039      6_104 0.000e+00  4290 0.000e+00  2.634
368759   rs9346818      6_104 0.000e+00  3538 0.000e+00  7.950
368862   rs1247539      6_104 0.000e+00  3483 0.000e+00 -4.294

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
368715  rs60425481      6_104    1.0000 34617.58 0.1007435  -7.113
368711   rs3106169      6_104    0.6210 34665.56 0.0626470  11.139
368720   rs3106167      6_104    0.4787 34665.13 0.0482930  11.136
368712   rs3127598      6_104    0.4710 34665.21 0.0475157  11.135
368803 rs374071816      6_104    0.9996  6415.76 0.0186626  16.254
368704  rs11755965      6_104    0.1257 34655.20 0.0126789  11.140
795634 rs147985405       19_9    0.9986  2286.17 0.0066440 -48.935
805501    rs814573      19_31    1.0000  2231.68 0.0064946  55.538
805506  rs12721109      19_31    1.0000  1355.57 0.0039450 -46.326
805450  rs62117204      19_31    1.0000   825.83 0.0024033 -44.672
805503 rs113345881      19_31    1.0000   781.13 0.0022732 -34.319
805468 rs111794050      19_31    1.0000   771.38 0.0022448 -33.600
68852     rs548145       2_13    1.0000   664.99 0.0019352  33.086
798144   rs3794991      19_15    1.0000   435.64 0.0012678 -21.492
68849     rs934197       2_13    1.0000   414.98 0.0012077  33.061
76524    rs4076834       2_27    0.9314   425.49 0.0011533 -20.109
281225   rs3843482       5_44    0.8372   395.85 0.0009645  25.034
14832    rs1887552       1_34    0.9063   344.07 0.0009075  -9.869
504532 rs115478735       9_70    1.0000   307.40 0.0008946  19.012
14831    rs2495502       1_34    1.0000   300.73 0.0008752   6.292
795642   rs1569372       19_9    0.9993   278.34 0.0008095  10.006
462713  rs79658059       8_83    0.9690   269.87 0.0007611 -16.022
368612  rs12208357      6_103    1.0000   244.15 0.0007105  12.282
795613  rs73013176       19_9    1.0000   240.92 0.0007011 -16.233
68843    rs1042034       2_13    1.0000   237.63 0.0006915  16.573
68929    rs1848922       2_13    1.0000   231.66 0.0006742  25.412
462724  rs13252684       8_83    1.0000   227.38 0.0006617  11.964
14849     rs471705       1_34    1.0000   210.38 0.0006122  16.263
281202  rs10062361       5_44    0.9869   202.05 0.0005803  20.321
805209  rs62115478      19_30    1.0000   183.16 0.0005330 -14.326
70579     rs780093       2_16    1.0000   167.21 0.0004866 -14.143
761781   rs8070232      17_39    1.0000   152.14 0.0004428  -8.091
368626   rs3818678      6_103    0.7665   197.23 0.0004399  -9.948
585721   rs3135506      11_70    0.9956   147.38 0.0004270  12.373
761755 rs113408695      17_39    1.0000   146.62 0.0004267  12.769
731346    rs821840      16_30    0.8951   163.02 0.0004247 -13.475
14842   rs10888896       1_34    1.0000   134.32 0.0003909  11.894
68794   rs11679386       2_12    1.0000   132.05 0.0003843  11.909
761766   rs9303012      17_39    0.8164   144.47 0.0003432   2.259
306104  rs12657266       5_92    0.7522   156.65 0.0003429  13.895
795651 rs137992968       19_9    1.0000   114.51 0.0003333 -10.753
443063   rs4738679       8_45    1.0000   108.15 0.0003147 -11.700
462712   rs2980875       8_83    0.5510   184.92 0.0002965 -22.102
806761    rs838145      19_33    0.9856    97.91 0.0002809 -11.874
625914    rs653178      12_67    0.9924    92.80 0.0002680  11.050
795637   rs3745677       19_9    0.9993    90.85 0.0002642   9.336
795718    rs322125      19_10    0.8873   101.66 0.0002625  -7.470
14801   rs11580527       1_34    1.0000    88.52 0.0002576 -11.167
821775  rs11086801      20_25    0.7818   106.07 0.0002413  10.975
821599   rs6102034      20_24    0.8443    96.35 0.0002367 -11.190

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
805501    rs814573      19_31 1.000e+00 2231.7 6.495e-03  55.54
795634 rs147985405       19_9 9.986e-01 2286.2 6.644e-03 -48.94
795629  rs73015020       19_9 8.132e-04 2273.9 5.381e-06 -48.80
795627 rs138175288       19_9 3.800e-04 2272.1 2.513e-06 -48.78
795628 rs138294113       19_9 9.208e-05 2268.2 6.078e-07 -48.75
795630  rs77140532       19_9 5.573e-05 2268.7 3.680e-07 -48.74
795631 rs112552009       19_9 2.794e-05 2264.7 1.841e-07 -48.71
795632  rs10412048       19_9 1.129e-05 2265.4 7.443e-08 -48.70
795626  rs55997232       19_9 2.986e-09 2245.0 1.951e-11 -48.52
805506  rs12721109      19_31 1.000e+00 1355.6 3.945e-03 -46.33
805450  rs62117204      19_31 1.000e+00  825.8 2.403e-03 -44.67
805437   rs1551891      19_31 0.000e+00  500.6 0.000e+00 -42.27
875656  rs12740374       1_67 5.982e-04 1473.3 2.565e-06 -41.79
875652   rs7528419       1_67 6.014e-04 1469.3 2.572e-06 -41.74
875663    rs646776       1_67 5.262e-04 1468.1 2.248e-06  41.73
875662    rs629301       1_67 4.946e-04 1464.4 2.108e-06  41.69
875674    rs583104       1_67 5.301e-04 1423.3 2.196e-06  41.09
875677   rs4970836       1_67 5.222e-04 1420.3 2.158e-06  41.05
875679   rs1277930       1_67 5.314e-04 1415.6 2.189e-06  40.98
875680    rs599839       1_67 5.444e-04 1414.6 2.241e-06  40.96
795635  rs17248769       19_9 1.328e-07 1721.5 6.655e-10 -40.84
795636   rs2228671       19_9 9.375e-08 1710.4 4.666e-10 -40.70
875660   rs3832016       1_67 4.039e-04 1375.1 1.616e-06  40.40
875657    rs660240       1_67 4.032e-04 1367.8 1.605e-06  40.29
875675    rs602633       1_67 4.386e-04 1346.1 1.718e-06  39.96
795625   rs9305020       19_9 3.120e-14 1305.6 1.185e-16 -34.84
805497    rs405509      19_31 0.000e+00  976.1 0.000e+00 -34.64
875643   rs4970834       1_67 7.888e-04 1014.8 2.329e-06 -34.62
805503 rs113345881      19_31 1.000e+00  781.1 2.273e-03 -34.32
805421  rs62120566      19_31 0.000e+00 1335.0 0.000e+00 -33.74
805468 rs111794050      19_31 1.000e+00  771.4 2.245e-03 -33.60
68852     rs548145       2_13 1.000e+00  665.0 1.935e-03  33.09
805474   rs4802238      19_31 0.000e+00  979.3 0.000e+00  33.08
68849     rs934197       2_13 1.000e+00  415.0 1.208e-03  33.06
805415 rs188099946      19_31 0.000e+00 1279.7 0.000e+00 -33.04
805485   rs2972559      19_31 0.000e+00 1308.1 0.000e+00  32.29
805409 rs201314191      19_31 0.000e+00 1186.6 0.000e+00 -32.07
875664   rs3902354       1_67 4.510e-04  866.7 1.138e-06  32.00
875653  rs11102967       1_67 4.528e-04  863.2 1.137e-06  31.94
875678   rs4970837       1_67 5.075e-04  859.4 1.269e-06  31.86
805476  rs56394238      19_31 0.000e+00  972.3 0.000e+00  31.55
805453   rs2965169      19_31 0.000e+00  361.2 0.000e+00 -31.38
805477   rs3021439      19_31 0.000e+00  865.7 0.000e+00  31.05
875648    rs611917       1_67 4.313e-04  812.6 1.020e-06 -30.98
68879   rs12997242       2_13 2.825e-11  382.6 3.145e-14  30.82
805484  rs12162222      19_31 0.000e+00 1120.2 0.000e+00  30.50
68853     rs478588       2_13 8.642e-11  612.9 1.541e-13  30.49
805414  rs62119327      19_31 0.000e+00 1044.9 0.000e+00 -30.42
68854   rs56350433       2_13 3.662e-12  350.9 3.740e-15  30.23
68859   rs56079819       2_13 3.669e-12  350.1 3.738e-15  30.19

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