LDL - Liver
sheng Qian
2022-10-18
Last updated: 2023-01-18
Checks: 5 2
Knit directory: cTWAS_analysis/
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Weight QC
[1] 11502[1] 4561
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
431 295 246 193 189 298 267 151 177 182 275 240 79 148 149 254 260 66 327 118
21 22
65 151 [1] 1Load ctwas results
Check convergence of parameters
gene snp
0.001363 0.003445 gene snp
14.35 13.82 [1] 0.3957[1] 343621[1] 4561 8696600 gene snp
0.0002597 1.2052259 [1] 1.205 gene
0.0002154 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$susie_pip>0.8), 20)) genename region_tag susie_pip mu2 PVE z num_eqtl
9251 ZNF329 19_39 0.9911 105.18 3.034e-04 10.436 1
10708 NYNRIN 14_3 0.9908 52.66 1.518e-04 7.679 1
1597 PLTP 20_28 0.9906 55.10 1.588e-04 -5.732 1
NA.1566 <NA> 8_12 0.9895 75.90 2.186e-04 10.465 1
9365 GAS6 13_62 0.9842 64.66 1.852e-04 -8.924 1
NA.1558 <NA> 4_98 0.9749 21.38 6.065e-05 4.304 1
9046 KLHDC7A 1_13 0.9636 19.43 5.449e-05 4.124 1
NA.1571 <NA> 11_12 0.9542 21.85 6.067e-05 4.388 1
5988 FADS1 11_34 0.9471 143.53 3.956e-04 12.675 1
9054 SPTY2D1 11_13 0.9442 30.46 8.371e-05 -5.587 1
1309 FMO2 1_84 0.9337 24.68 6.707e-05 4.838 1
NA.1552 <NA> 1_121 0.9290 186.89 5.053e-04 -15.074 1
NA.1602 <NA> 19_33 0.9285 42.02 1.135e-04 8.642 1
11257 CYP2A6 19_28 0.9161 30.31 8.080e-05 5.407 1
9827 PALM3 19_11 0.9125 18.48 4.908e-05 3.839 1
6855 ALDH16A1 19_34 0.8984 27.53 7.197e-05 -4.119 1
8418 GNB2 7_62 0.8981 26.97 7.049e-05 5.813 1
10459 PRMT6 1_66 0.8975 29.95 7.823e-05 -5.374 1
2454 ST3GAL4 11_77 0.8972 72.70 1.898e-04 11.734 1
1320 CWF19L1 10_64 0.8895 31.89 8.256e-05 5.707 1
2092 SP4 7_19 0.8856 92.07 2.373e-04 10.701 1
697 PIGB 15_24 0.8813 17.38 4.456e-05 3.665 1
NA.1562 <NA> 6_21 0.8703 48.78 1.235e-04 -7.441 1
7918 PDHB 3_40 0.8640 24.67 6.204e-05 3.304 1
3714 SLC2A4RG 20_38 0.8578 29.93 7.471e-05 -5.563 1
3659 GNMT 6_33 0.8545 26.26 6.530e-05 5.058 1
1114 SRRT 7_62 0.8384 28.55 6.967e-05 5.938 1
NA.1595 <NA> 18_35 0.8327 17.91 4.340e-05 -3.607 1
NA.1559 <NA> 5_78 0.8320 17.53 4.245e-05 -3.817 1
10429 PNP 14_1 0.8262 17.41 4.185e-05 -3.575 1
4669 SCYL2 12_59 0.8248 17.35 4.165e-05 -3.564 1
7542 LIPC 15_26 0.8190 62.35 1.486e-04 -7.731 1
7092 NEK10 3_20 0.8098 21.08 4.968e-05 -4.089 1Genes with largest effect sizes
#plot PIP vs effect size
plot(ctwas_gene_res$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
10399 LPA 6_104 0.000e+00 13872.0 0.000e+00 6.319 1
5797 SLC22A3 6_104 0.000e+00 10063.2 0.000e+00 -6.225 1
NA.1412 <NA> 19_31 0.000e+00 1285.6 0.000e+00 -11.297 1
NA.58 <NA> 1_67 6.307e-01 792.3 1.454e-03 -41.793 1
NA.57 <NA> 1_67 6.307e-01 792.3 1.454e-03 -41.793 1
4433 PSRC1 1_67 6.307e-01 792.3 1.454e-03 -41.793 1
NA.579 <NA> 6_104 0.000e+00 458.0 0.000e+00 -4.654 1
NA.578 <NA> 6_104 0.000e+00 439.6 0.000e+00 -8.475 1
3270 ALDH6A1 14_34 2.361e-01 271.5 1.865e-04 4.361 1
5166 PTGR2 14_34 3.984e-04 265.6 3.079e-07 -3.091 1
NA.152 <NA> 2_13 6.321e-11 247.9 4.561e-14 -4.702 1
5375 GEMIN7 19_31 0.000e+00 246.5 0.000e+00 14.336 1
8026 PCSK9 1_34 3.015e-01 207.3 1.819e-04 16.079 1
4315 ANGPTL3 1_39 9.117e-02 201.5 5.347e-05 15.169 1
NA.1552 <NA> 1_121 9.290e-01 186.9 5.053e-04 -15.074 1
NA.1567 <NA> 8_83 1.154e-01 161.1 5.411e-05 17.282 1
2077 ATP13A1 19_15 4.149e-01 148.9 1.798e-04 -13.541 1
10549 HLA-DMA 6_27 6.234e-03 148.6 2.696e-06 -2.364 1
8700 ABO 9_70 7.187e-02 146.7 3.068e-05 12.100 1
5988 FADS1 11_34 9.471e-01 143.5 3.956e-04 12.675 1Genes with highest PVE
#genes with 20 highest pve
head(ctwas_gene_res[order(-ctwas_gene_res$PVE),report_cols],20) genename region_tag susie_pip mu2 PVE z num_eqtl
NA.58 <NA> 1_67 0.6307 792.32 1.454e-03 -41.793 1
4433 PSRC1 1_67 0.6307 792.32 1.454e-03 -41.793 1
NA.57 <NA> 1_67 0.6307 792.32 1.454e-03 -41.793 1
NA.1552 <NA> 1_121 0.9290 186.89 5.053e-04 -15.074 1
5988 FADS1 11_34 0.9471 143.53 3.956e-04 12.675 1
9251 ZNF329 19_39 0.9911 105.18 3.034e-04 10.436 1
2092 SP4 7_19 0.8856 92.07 2.373e-04 10.701 1
NA.1566 <NA> 8_12 0.9895 75.90 2.186e-04 10.465 1
2454 ST3GAL4 11_77 0.8972 72.70 1.898e-04 11.734 1
3270 ALDH6A1 14_34 0.2361 271.52 1.865e-04 4.361 1
9365 GAS6 13_62 0.9842 64.66 1.852e-04 -8.924 1
8026 PCSK9 1_34 0.3015 207.31 1.819e-04 16.079 1
2077 ATP13A1 19_15 0.4149 148.91 1.798e-04 -13.541 1
1597 PLTP 20_28 0.9906 55.10 1.588e-04 -5.732 1
6090 CSNK1G3 5_75 0.7432 71.55 1.548e-04 8.881 1
10708 NYNRIN 14_3 0.9908 52.66 1.518e-04 7.679 1
7542 LIPC 15_26 0.8190 62.35 1.486e-04 -7.731 1
NA.1562 <NA> 6_21 0.8703 48.78 1.235e-04 -7.441 1
NA.1602 <NA> 19_33 0.9285 42.02 1.135e-04 8.642 1
NA.525 <NA> 6_26 0.7386 41.66 8.955e-05 6.638 1Genes with largest z scores
#genes with 20 largest z scores
head(ctwas_gene_res[order(-abs(ctwas_gene_res$z)),report_cols],20) genename region_tag susie_pip mu2 PVE z num_eqtl
4433 PSRC1 1_67 0.63068 792.32 1.454e-03 -41.79 1
NA.58 <NA> 1_67 0.63068 792.32 1.454e-03 -41.79 1
NA.57 <NA> 1_67 0.63068 792.32 1.454e-03 -41.79 1
NA.1567 <NA> 8_83 0.11545 161.06 5.411e-05 17.28 1
NA.1411 <NA> 19_31 0.00000 114.93 0.000e+00 16.27 1
8026 PCSK9 1_34 0.30153 207.31 1.819e-04 16.08 1
4315 ANGPTL3 1_39 0.09117 201.51 5.347e-05 15.17 1
NA.1552 <NA> 1_121 0.92904 186.89 5.053e-04 -15.07 1
5375 GEMIN7 19_31 0.00000 246.54 0.000e+00 14.34 1
2077 ATP13A1 19_15 0.41491 148.91 1.798e-04 -13.54 1
5988 FADS1 11_34 0.94713 143.53 3.956e-04 12.67 1
11016 APOC2 19_31 0.00000 87.17 0.000e+00 -12.21 1
8700 ABO 9_70 0.07187 146.70 3.068e-05 12.10 1
2454 ST3GAL4 11_77 0.89716 72.70 1.898e-04 11.73 1
NA.1412 <NA> 19_31 0.00000 1285.60 0.000e+00 -11.30 1
10926 FADS3 11_34 0.03054 109.13 9.697e-06 11.07 1
6183 POC5 5_44 0.01521 75.21 3.330e-06 10.86 1
2092 SP4 7_19 0.88562 92.07 2.373e-04 10.70 1
NA.1566 <NA> 8_12 0.98951 75.90 2.186e-04 10.46 1
9251 ZNF329 19_39 0.99107 105.18 3.034e-04 10.44 1Comparing 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$z) > sig_thresh)[1] 144#proportion of significant z scores
mean(abs(ctwas_gene_res$z) > sig_thresh)[1] 0.03157#genes with most significant z scores
head(ctwas_gene_res[order(-abs(ctwas_gene_res$z)),report_cols],20) genename region_tag susie_pip mu2 PVE z num_eqtl
4433 PSRC1 1_67 0.63068 792.32 1.454e-03 -41.79 1
NA.58 <NA> 1_67 0.63068 792.32 1.454e-03 -41.79 1
NA.57 <NA> 1_67 0.63068 792.32 1.454e-03 -41.79 1
NA.1567 <NA> 8_83 0.11545 161.06 5.411e-05 17.28 1
NA.1411 <NA> 19_31 0.00000 114.93 0.000e+00 16.27 1
8026 PCSK9 1_34 0.30153 207.31 1.819e-04 16.08 1
4315 ANGPTL3 1_39 0.09117 201.51 5.347e-05 15.17 1
NA.1552 <NA> 1_121 0.92904 186.89 5.053e-04 -15.07 1
5375 GEMIN7 19_31 0.00000 246.54 0.000e+00 14.34 1
2077 ATP13A1 19_15 0.41491 148.91 1.798e-04 -13.54 1
5988 FADS1 11_34 0.94713 143.53 3.956e-04 12.67 1
11016 APOC2 19_31 0.00000 87.17 0.000e+00 -12.21 1
8700 ABO 9_70 0.07187 146.70 3.068e-05 12.10 1
2454 ST3GAL4 11_77 0.89716 72.70 1.898e-04 11.73 1
NA.1412 <NA> 19_31 0.00000 1285.60 0.000e+00 -11.30 1
10926 FADS3 11_34 0.03054 109.13 9.697e-06 11.07 1
6183 POC5 5_44 0.01521 75.21 3.330e-06 10.86 1
2092 SP4 7_19 0.88562 92.07 2.373e-04 10.70 1
NA.1566 <NA> 8_12 0.98951 75.90 2.186e-04 10.46 1
9251 ZNF329 19_39 0.99107 105.18 3.034e-04 10.44 1SNPs with highest PIPs
#snps with PIP>0.8 or 20 highest PIPs
head(ctwas_snp_res[order(-ctwas_snp_res$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 332.73 9.683e-04 6.2922
71615 rs1042034 2_13 1.0000 245.67 7.150e-04 16.5730
71621 rs934197 2_13 1.0000 414.32 1.206e-03 33.0609
73351 rs780093 2_16 1.0000 171.27 4.984e-04 -14.1426
326429 rs115740542 6_20 1.0000 173.33 5.044e-04 -12.5323
370483 rs12208357 6_103 1.0000 258.29 7.517e-04 12.2823
370586 rs60425481 6_104 1.0000 60183.84 1.751e-01 -7.1125
681906 rs369107859 14_34 1.0000 1114.44 3.243e-03 -2.2480
760369 rs113408695 17_39 1.0000 151.54 4.410e-04 12.7688
793785 rs73013176 19_9 1.0000 247.78 7.211e-04 -16.2327
803622 rs62117204 19_31 1.0000 826.54 2.405e-03 -44.6722
803640 rs111794050 19_31 1.0000 785.66 2.286e-03 -33.5996
803673 rs814573 19_31 1.0000 2281.68 6.640e-03 55.5379
803675 rs113345881 19_31 1.0000 797.59 2.321e-03 -34.3186
803678 rs12721109 19_31 1.0000 1381.86 4.021e-03 -46.3258
901885 rs67138090 6_27 1.0000 992.82 2.889e-03 4.4111
796316 rs3794991 19_15 1.0000 442.70 1.288e-03 -21.4921
760395 rs8070232 17_39 1.0000 167.47 4.874e-04 -8.0915
927624 rs28601761 8_83 1.0000 344.17 1.002e-03 -25.2552
71566 rs11679386 2_12 1.0000 147.55 4.294e-04 11.9094
71701 rs1848922 2_13 1.0000 235.16 6.843e-04 25.4123
71624 rs548145 2_13 1.0000 680.92 1.982e-03 33.0860
498465 rs2437818 9_53 1.0000 73.83 2.149e-04 6.3340
507180 rs115478735 9_70 1.0000 316.48 9.210e-04 19.0118
1050051 rs1800961 20_28 1.0000 74.64 2.172e-04 -8.8970
804013 rs150262789 19_32 1.0000 78.29 2.278e-04 -10.8985
759453 rs1801689 17_38 1.0000 83.52 2.431e-04 9.3964
803336 rs73036721 19_30 1.0000 60.41 1.758e-04 -7.7879
733684 rs12149380 16_38 1.0000 116.77 3.398e-04 -4.1646
445977 rs4738679 8_45 1.0000 111.18 3.236e-04 -11.6999
277956 rs1499279 5_30 1.0000 64.24 1.870e-04 -8.3746
79416 rs72800939 2_28 1.0000 57.55 1.675e-04 -7.8457
793823 rs137992968 19_9 1.0000 117.97 3.433e-04 -10.7526
14842 rs10888896 1_34 1.0000 139.19 4.051e-04 11.8938
390727 rs217396 7_32 1.0000 79.68 2.319e-04 -9.4286
7646 rs79598313 1_18 1.0000 48.22 1.403e-04 7.0246
444582 rs140753685 8_42 1.0000 57.34 1.669e-04 7.7992
803381 rs62115478 19_30 1.0000 188.87 5.496e-04 -14.3262
54930 rs2807848 1_112 1.0000 56.91 1.656e-04 -7.8828
14801 rs11580527 1_34 1.0000 89.87 2.615e-04 -11.1672
351920 rs9496567 6_67 1.0000 39.94 1.162e-04 -6.3402
326408 rs72834643 6_20 1.0000 46.33 1.348e-04 -6.0487
927640 rs112875651 8_83 0.9999 304.74 8.868e-04 -24.2936
322700 rs11376017 6_13 0.9999 67.55 1.966e-04 -8.5079
796347 rs113619686 19_15 0.9999 60.05 1.747e-04 0.5939
793849 rs4804149 19_10 0.9998 47.55 1.383e-04 6.5194
326806 rs454182 6_22 0.9997 39.06 1.136e-04 4.7791
79280 rs139029940 2_27 0.9997 39.87 1.160e-04 6.8150
370674 rs374071816 6_104 0.9996 10997.56 3.199e-02 16.2541
733727 rs57186116 16_38 0.9995 69.78 2.030e-04 7.7146
793814 rs1569372 19_9 0.9995 296.29 8.618e-04 10.0055
793902 rs322144 19_10 0.9995 61.07 1.776e-04 3.9466
544257 rs17875416 10_71 0.9994 39.04 1.135e-04 -6.2663
610248 rs7397189 12_36 0.9991 35.03 1.018e-04 -5.7710
498438 rs2297400 9_53 0.9990 41.96 1.220e-04 6.6057
284408 rs7701166 5_44 0.9990 35.62 1.035e-04 -2.4848
793806 rs147985405 19_9 0.9988 2365.82 6.877e-03 -48.9352
795956 rs2302209 19_14 0.9984 44.07 1.280e-04 6.6360
434309 rs1495743 8_20 0.9981 41.94 1.218e-04 -6.5160
586639 rs3135506 11_70 0.9961 151.89 4.403e-04 12.3730
327243 rs3130253 6_23 0.9958 31.05 8.999e-05 5.6415
586644 rs75542613 11_70 0.9957 36.43 1.056e-04 -6.5344
817766 rs76981217 20_24 0.9956 35.73 1.035e-04 7.6925
445945 rs56386732 8_45 0.9954 35.14 1.018e-04 -7.0123
626240 rs653178 12_67 0.9938 98.55 2.850e-04 11.0501
739179 rs2255451 16_48 0.9928 37.18 1.074e-04 -6.3628
614614 rs148481241 12_44 0.9904 28.03 8.080e-05 5.0955
284349 rs10062361 5_44 0.9902 211.80 6.104e-04 20.3206
328028 rs28780090 6_24 0.9879 51.27 1.474e-04 6.8714
142216 rs709149 3_9 0.9876 37.26 1.071e-04 -6.7820
793809 rs3745677 19_9 0.9831 95.43 2.730e-04 9.3358
148862 rs9834932 3_24 0.9828 66.91 1.914e-04 -8.4816
817717 rs6029132 20_24 0.9827 40.18 1.149e-04 -6.7625
407105 rs3197597 7_61 0.9772 29.65 8.432e-05 -5.0452
630329 rs11057830 12_76 0.9759 26.42 7.503e-05 4.9296
817770 rs73124945 20_24 0.9750 32.38 9.188e-05 -7.7754
803996 rs34942359 19_32 0.9740 64.45 1.827e-04 -7.0096
247763 rs114756490 4_100 0.9718 26.49 7.492e-05 4.9889
390777 rs141379002 7_33 0.9647 26.18 7.350e-05 4.8970
899271 rs34723862 6_21 0.9634 34.90 9.785e-05 -6.3369
225584 rs1458038 4_54 0.9623 53.78 1.506e-04 -7.4179
472926 rs7024888 9_3 0.9611 26.21 7.331e-05 -5.0558
480790 rs1556516 9_16 0.9608 75.51 2.111e-04 -8.9921
825487 rs62219001 21_2 0.9595 26.69 7.452e-05 -4.9484
595271 rs11048034 12_9 0.9592 36.25 1.012e-04 6.1337
570268 rs6591179 11_36 0.9550 26.58 7.386e-05 4.8933
763528 rs4969183 17_44 0.9545 50.25 1.396e-04 7.1693
629194 rs1169300 12_74 0.9482 69.65 1.922e-04 8.6855
624333 rs1196760 12_63 0.9474 26.37 7.269e-05 -4.8667
79296 rs4076834 2_27 0.9451 444.69 1.223e-03 -20.1086
79293 rs13430143 2_27 0.9434 84.73 2.326e-04 -3.3445
326247 rs75080831 6_19 0.9427 58.13 1.595e-04 -7.9067
327214 rs28986304 6_23 0.9338 42.06 1.143e-04 7.3825
197209 rs5855544 3_120 0.9290 24.05 6.502e-05 -4.5937
733725 rs9652628 16_38 0.9281 129.99 3.511e-04 11.9505
198996 rs36205397 4_4 0.9236 41.81 1.124e-04 6.1594
429986 rs117037226 8_11 0.9221 24.58 6.596e-05 4.1922
749912 rs117859452 17_17 0.9198 24.90 6.664e-05 -3.8517
370477 rs9456502 6_103 0.9168 33.67 8.982e-05 5.9640
803913 rs377297589 19_32 0.9157 51.61 1.375e-04 -6.7865
71618 rs78610189 2_13 0.9123 60.75 1.613e-04 -8.3855
173034 rs189174 3_74 0.9061 42.08 1.109e-04 6.7678
14832 rs1887552 1_34 0.9045 376.56 9.912e-04 -9.8686
512130 rs10905277 10_8 0.9030 28.39 7.460e-05 5.1258
730027 rs821840 16_30 0.8996 168.75 4.418e-04 -13.4753
354656 rs12199109 6_73 0.8969 25.55 6.670e-05 4.8570
543968 rs12244851 10_70 0.8968 37.82 9.871e-05 -4.8831
793890 rs322125 19_10 0.8926 107.56 2.794e-04 -7.4704
809040 rs74273659 20_5 0.8904 25.06 6.493e-05 4.6468
639216 rs1012130 13_10 0.8890 41.95 1.085e-04 -2.7810
498458 rs2777788 9_53 0.8845 61.09 1.573e-04 -5.7370
582908 rs201912654 11_59 0.8777 40.92 1.045e-04 -6.3056
124313 rs7569317 2_120 0.8763 43.14 1.100e-04 7.9007
201221 rs2002574 4_10 0.8729 25.20 6.401e-05 -4.5583
821269 rs10641149 20_32 0.8659 27.71 6.982e-05 5.0758
832728 rs2835302 21_16 0.8649 25.83 6.501e-05 -4.6537
749821 rs3032928 17_17 0.8621 34.29 8.604e-05 6.1119
488776 rs11144506 9_35 0.8580 27.41 6.844e-05 5.0427
284372 rs3843482 5_44 0.8463 414.44 1.021e-03 25.0344
71418 rs6531234 2_12 0.8458 42.74 1.052e-04 -7.1708
817735 rs6102034 20_24 0.8442 98.91 2.430e-04 -11.1900
755040 rs4793601 17_28 0.8429 31.10 7.628e-05 -6.2095
793859 rs58495388 19_10 0.8423 34.64 8.492e-05 5.5313
760380 rs9303012 17_39 0.8341 162.51 3.945e-04 2.2591
360859 rs9321207 6_86 0.8336 31.32 7.599e-05 5.4016
99983 rs138192199 2_69 0.8246 26.29 6.309e-05 4.6708
639208 rs1799955 13_10 0.8219 73.95 1.769e-04 -6.6936
833865 rs149577713 21_19 0.8044 30.24 7.079e-05 3.3168
237480 rs138204164 4_77 0.8041 27.11 6.345e-05 -4.8489
733665 rs12708919 16_38 0.8039 146.87 3.436e-04 11.3028
501036 rs2762469 9_56 0.8004 25.97 6.048e-05 -4.5317
844816 rs145678077 22_17 0.8002 26.35 6.137e-05 -4.8686SNPs 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
370582 rs3106169 6_104 6.673e-01 60236 1.170e-01 11.139
370583 rs3127598 6_104 4.732e-01 60236 8.295e-02 11.135
370591 rs3106167 6_104 4.774e-01 60236 8.369e-02 11.136
370575 rs11755965 6_104 5.036e-02 60218 8.825e-03 11.140
370586 rs60425481 6_104 1.000e+00 60184 1.751e-01 -7.113
370566 rs12194962 6_104 8.032e-11 60090 1.405e-11 11.106
370584 rs3127597 6_104 1.438e-12 60051 2.513e-13 11.145
370545 rs3119311 6_104 0.000e+00 43583 0.000e+00 8.031
370539 rs3127579 6_104 0.000e+00 31731 0.000e+00 7.568
370533 rs10945658 6_104 0.000e+00 27759 0.000e+00 8.309
370532 rs3119308 6_104 0.000e+00 27691 0.000e+00 8.274
370528 rs3103352 6_104 0.000e+00 27689 0.000e+00 8.522
370524 rs3101821 6_104 0.000e+00 27592 0.000e+00 8.528
370530 rs12205178 6_104 0.000e+00 27534 0.000e+00 8.297
370522 rs148015788 6_104 0.000e+00 27183 0.000e+00 8.351
370633 rs3124784 6_104 0.000e+00 22764 0.000e+00 9.680
370634 rs3127596 6_104 0.000e+00 20650 0.000e+00 9.556
370627 rs3127599 6_104 0.000e+00 20554 0.000e+00 9.259
370597 rs2481030 6_104 0.000e+00 19757 0.000e+00 4.811
370562 rs2504949 6_104 0.000e+00 16278 0.000e+00 2.937
370615 rs388170 6_104 0.000e+00 15068 0.000e+00 3.833
370537 rs316013 6_104 0.000e+00 14446 0.000e+00 -3.002
370538 rs316012 6_104 0.000e+00 14272 0.000e+00 -3.074
370618 rs9355288 6_104 0.000e+00 13941 0.000e+00 6.319
370526 rs610206 6_104 0.000e+00 13190 0.000e+00 -2.944
370527 rs595374 6_104 0.000e+00 13165 0.000e+00 -2.921
370534 rs315995 6_104 0.000e+00 12844 0.000e+00 -3.207
370531 rs543435 6_104 0.000e+00 12796 0.000e+00 -3.250
370580 rs452867 6_104 0.000e+00 12038 0.000e+00 -7.124
370589 rs367334 6_104 0.000e+00 12029 0.000e+00 -7.106
370577 rs589931 6_104 0.000e+00 12028 0.000e+00 -7.116
370578 rs600584 6_104 0.000e+00 12028 0.000e+00 -7.113
370579 rs434953 6_104 0.000e+00 12027 0.000e+00 -7.111
370585 rs380498 6_104 0.000e+00 12027 0.000e+00 -7.115
370553 rs3119312 6_104 0.000e+00 11551 0.000e+00 3.771
370674 rs374071816 6_104 9.996e-01 10998 3.199e-02 16.254
370612 rs2872317 6_104 0.000e+00 10577 0.000e+00 6.746
370609 rs2313453 6_104 0.000e+00 10569 0.000e+00 6.718
370679 rs4252185 6_104 3.537e-04 10130 1.043e-05 15.878
370600 rs146184004 6_104 0.000e+00 10102 0.000e+00 6.534
370603 rs624319 6_104 0.000e+00 9950 0.000e+00 -6.291
370602 rs637614 6_104 0.000e+00 9935 0.000e+00 -6.362
370604 rs486339 6_104 0.000e+00 9867 0.000e+00 -6.311
370549 rs316036 6_104 0.000e+00 9681 0.000e+00 -7.009
370601 rs555754 6_104 0.000e+00 9611 0.000e+00 -6.593
370680 rs12212146 6_104 0.000e+00 7719 0.000e+00 -2.410
370547 rs582280 6_104 0.000e+00 7472 0.000e+00 2.635
370546 rs497039 6_104 0.000e+00 7470 0.000e+00 2.634
370733 rs1247539 6_104 0.000e+00 6051 0.000e+00 -4.294
370630 rs9346818 6_104 0.000e+00 6042 0.000e+00 7.950SNPs 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
370586 rs60425481 6_104 1.00000 60183.8 0.1751460 -7.1125
370582 rs3106169 6_104 0.66731 60236.3 0.1169784 11.1387
370591 rs3106167 6_104 0.47741 60235.7 0.0836877 11.1356
370583 rs3127598 6_104 0.47321 60235.9 0.0829522 11.1347
370674 rs374071816 6_104 0.99965 10997.6 0.0319936 16.2541
370575 rs11755965 6_104 0.05036 60217.8 0.0088253 11.1396
793806 rs147985405 19_9 0.99884 2365.8 0.0068770 -48.9352
803673 rs814573 19_31 1.00000 2281.7 0.0066401 55.5379
803678 rs12721109 19_31 1.00000 1381.9 0.0040215 -46.3258
681906 rs369107859 14_34 1.00000 1114.4 0.0032432 -2.2480
901885 rs67138090 6_27 1.00000 992.8 0.0028893 4.4111
803622 rs62117204 19_31 1.00000 826.5 0.0024054 -44.6722
803675 rs113345881 19_31 1.00000 797.6 0.0023211 -34.3186
803640 rs111794050 19_31 1.00000 785.7 0.0022864 -33.5996
71624 rs548145 2_13 1.00000 680.9 0.0019816 33.0860
681915 rs2159704 14_34 0.48667 1108.3 0.0015697 1.2852
901775 rs9275698 6_27 0.52550 969.7 0.0014830 -0.6590
796316 rs3794991 19_15 1.00000 442.7 0.0012883 -21.4921
79296 rs4076834 2_27 0.94506 444.7 0.0012230 -20.1086
71621 rs934197 2_13 1.00000 414.3 0.0012057 33.0609
681923 rs7144134 14_34 0.75679 468.0 0.0010307 4.3724
284372 rs3843482 5_44 0.84633 414.4 0.0010208 25.0344
927624 rs28601761 8_83 1.00000 344.2 0.0010016 -25.2552
14832 rs1887552 1_34 0.90447 376.6 0.0009912 -9.8686
681903 rs7156583 14_34 0.30305 1108.4 0.0009776 1.2485
14831 rs2495502 1_34 1.00000 332.7 0.0009683 6.2922
507180 rs115478735 9_70 1.00000 316.5 0.0009210 19.0118
927640 rs112875651 8_83 0.99990 304.7 0.0008868 -24.2936
793814 rs1569372 19_9 0.99947 296.3 0.0008618 10.0055
370483 rs12208357 6_103 1.00000 258.3 0.0007517 12.2823
793785 rs73013176 19_9 1.00000 247.8 0.0007211 -16.2327
71615 rs1042034 2_13 1.00000 245.7 0.0007150 16.5730
902341 rs2859088 6_27 0.24594 963.6 0.0006896 -0.7222
71701 rs1848922 2_13 1.00000 235.2 0.0006843 25.4123
902323 rs2858883 6_27 0.22875 962.9 0.0006410 -0.7327
284349 rs10062361 5_44 0.99024 211.8 0.0006104 20.3206
803381 rs62115478 19_30 1.00000 188.9 0.0005496 -14.3262
326429 rs115740542 6_20 1.00000 173.3 0.0005044 -12.5323
73351 rs780093 2_16 1.00000 171.3 0.0004984 -14.1426
760395 rs8070232 17_39 1.00000 167.5 0.0004874 -8.0915
370497 rs3818678 6_103 0.77281 210.3 0.0004729 -9.9478
730027 rs821840 16_30 0.89964 168.7 0.0004418 -13.4753
760369 rs113408695 17_39 1.00000 151.5 0.0004410 12.7688
14849 rs471705 1_34 0.69846 216.8 0.0004407 16.2630
586639 rs3135506 11_70 0.99609 151.9 0.0004403 12.3730
71566 rs11679386 2_12 1.00000 147.5 0.0004294 11.9094
14842 rs10888896 1_34 1.00000 139.2 0.0004051 11.8938
760380 rs9303012 17_39 0.83414 162.5 0.0003945 2.2591
681913 rs72627160 14_34 0.12065 1107.0 0.0003887 1.2216
308950 rs12657266 5_92 0.76084 164.1 0.0003634 13.8948SNPs 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
803673 rs814573 19_31 1.000e+00 2281.7 6.640e-03 55.54
793806 rs147985405 19_9 9.988e-01 2365.8 6.877e-03 -48.94
793801 rs73015020 19_9 6.902e-04 2352.9 4.726e-06 -48.80
793799 rs138175288 19_9 3.187e-04 2351.1 2.181e-06 -48.78
793800 rs138294113 19_9 7.476e-05 2347.4 5.107e-07 -48.75
793802 rs77140532 19_9 4.455e-05 2347.5 3.043e-07 -48.74
793803 rs112552009 19_9 2.272e-05 2344.2 1.550e-07 -48.71
793804 rs10412048 19_9 8.708e-06 2344.2 5.941e-08 -48.70
793798 rs55997232 19_9 1.304e-09 2324.3 8.823e-12 -48.52
803678 rs12721109 19_31 1.000e+00 1381.9 4.021e-03 -46.33
803622 rs62117204 19_31 1.000e+00 826.5 2.405e-03 -44.67
803609 rs1551891 19_31 0.000e+00 493.3 0.000e+00 -42.27
793807 rs17248769 19_9 2.192e-09 1779.7 1.135e-11 -40.84
793808 rs2228671 19_9 1.621e-09 1768.6 8.344e-12 -40.70
793797 rs9305020 19_9 2.565e-14 1356.8 1.013e-16 -34.84
803669 rs405509 19_31 0.000e+00 974.0 0.000e+00 -34.64
803675 rs113345881 19_31 1.000e+00 797.6 2.321e-03 -34.32
803593 rs62120566 19_31 0.000e+00 1358.5 0.000e+00 -33.74
803640 rs111794050 19_31 1.000e+00 785.7 2.286e-03 -33.60
71624 rs548145 2_13 1.000e+00 680.9 1.982e-03 33.09
803646 rs4802238 19_31 0.000e+00 981.0 0.000e+00 33.08
71621 rs934197 2_13 1.000e+00 414.3 1.206e-03 33.06
803587 rs188099946 19_31 0.000e+00 1302.0 0.000e+00 -33.04
803657 rs2972559 19_31 0.000e+00 1323.4 0.000e+00 32.29
803581 rs201314191 19_31 0.000e+00 1206.8 0.000e+00 -32.07
803648 rs56394238 19_31 0.000e+00 977.4 0.000e+00 31.55
803625 rs2965169 19_31 0.000e+00 350.4 0.000e+00 -31.38
803649 rs3021439 19_31 0.000e+00 867.2 0.000e+00 31.05
30850 rs611917 1_67 3.284e-03 436.1 4.168e-06 -30.98
71651 rs12997242 2_13 9.647e-12 379.9 1.067e-14 30.82
803656 rs12162222 19_31 0.000e+00 1131.9 0.000e+00 30.50
71625 rs478588 2_13 4.707e-11 628.4 8.609e-14 30.49
803586 rs62119327 19_31 0.000e+00 1061.9 0.000e+00 -30.42
71626 rs56350433 2_13 1.753e-12 350.5 1.788e-15 30.23
71631 rs56079819 2_13 1.755e-12 349.7 1.786e-15 30.19
71635 rs2337383 2_13 1.715e-12 342.3 1.708e-15 29.89
71636 rs56090741 2_13 1.717e-12 341.8 1.707e-15 29.86
71640 rs7568899 2_13 1.677e-12 333.1 1.625e-15 29.70
71641 rs62135036 2_13 1.675e-12 332.8 1.622e-15 29.69
71647 rs11687710 2_13 1.682e-12 332.0 1.625e-15 29.63
71652 rs532300 2_13 7.166e-12 576.2 1.202e-14 29.57
71653 rs558130 2_13 7.166e-12 576.2 1.202e-14 29.57
71654 rs533211 2_13 7.166e-12 576.2 1.202e-14 29.57
71675 rs574461 2_13 7.306e-12 575.8 1.224e-14 29.57
71677 rs494465 2_13 7.265e-12 575.7 1.217e-14 29.56
71655 rs528113 2_13 7.124e-12 575.9 1.194e-14 29.56
71660 rs1652418 2_13 7.107e-12 575.6 1.190e-14 29.56
71662 rs563696 2_13 7.079e-12 575.5 1.185e-14 29.56
71650 rs312979 2_13 6.932e-12 575.4 1.161e-14 29.56
71664 rs479545 2_13 6.976e-12 575.1 1.168e-14 29.55
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