LDL - Liver
sheng Qian
2022-10-18
Last updated: 2023-01-23
Checks: 5 2
Knit directory: cTWAS_analysis/
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Weight QC
[1] 11502[1] 3520
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
338 238 180 136 147 231 190 122 131 131 214 195 61 110 115 193 215 50 269 99
21 22
48 107 [1] 0.7656Load ctwas results
Check convergence of parameters
| Version | Author | Date |
|---|---|---|
| 4d68754 | sq-96 | 2023-01-23 |
#estimated group prior
estimated_group_prior <- estimated_group_prior_all[,ncol(group_prior_rec)]
print(estimated_group_prior) SNP gene
0.0001653 0.0235915 #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
11.52 38.25 #estimated enrichment
estimated_enrichment <- estimated_enrichment_all[ncol(group_prior_var_rec)]
print(estimated_enrichment)[1] 142.8#report sample size
print(sample_size)[1] 343621#report group size
print(group_size) SNP gene
8696600 3520 #estimated group PVE
estimated_group_pve <- estimated_group_pve_all[,ncol(group_prior_rec)]
print(estimated_group_pve) SNP gene
0.048163 0.009244 #total PVE
sum(estimated_group_pve)[1] 0.05741#attributable PVE
estimated_group_pve/sum(estimated_group_pve) SNP gene
0.839 0.161 Genes with highest PIPs
#distribution of PIPs
hist(ctwas_gene_res$susie_pip, xlim=c(0,1), main="Distribution of Gene PIPs")
| Version | Author | Date |
|---|---|---|
| 4d68754 | sq-96 | 2023-01-23 |
#genes with PIP>0.8 or 20 highest PIPs
head(ctwas_gene_res[order(-ctwas_gene_res$susie_pip),report_cols], max(sum(ctwas_gene_res$susie_pip>0.8), 20)) genename region_tag susie_pip mu2 PVE z num_eqtl
4433 PSRC1 1_67 1.0000 1652.10 4.808e-03 -41.687 1
2454 ST3GAL4 11_77 1.0000 172.26 5.013e-04 13.376 2
11327 HPR 16_38 1.0000 160.58 4.673e-04 -17.963 2
3720 INSIG2 2_69 1.0000 68.08 1.981e-04 -8.983 3
5988 FADS1 11_34 0.9999 163.14 4.747e-04 12.926 2
NA.407 <NA> 1_121 0.9995 202.13 5.879e-04 -15.108 1
10612 TRIM39 6_24 0.9990 70.98 2.064e-04 8.840 3
8523 TNKS 8_12 0.9942 74.80 2.164e-04 11.039 2
1597 PLTP 20_28 0.9940 60.45 1.749e-04 -5.732 1
5542 CNIH4 1_114 0.9931 40.46 1.170e-04 6.146 2
4315 ANGPTL3 1_39 0.9929 248.11 7.170e-04 16.132 1
9365 GAS6 13_62 0.9927 70.41 2.034e-04 -8.924 1
1999 PRKD2 19_33 0.9925 29.70 8.579e-05 5.072 2
3754 RRBP1 20_13 0.9924 32.02 9.247e-05 7.008 2
11257 CYP2A6 19_28 0.9842 32.38 9.274e-05 5.407 1
6090 CSNK1G3 5_75 0.9830 83.47 2.388e-04 9.116 1
2092 SP4 7_19 0.9817 101.51 2.900e-04 10.693 1
6387 TTC39B 9_13 0.9777 22.85 6.502e-05 -4.334 3
1114 SRRT 7_62 0.9732 32.63 9.241e-05 5.425 2
6774 PKN3 9_66 0.9504 47.07 1.302e-04 -6.621 1
1009 GSK3B 3_74 0.9351 42.24 1.149e-04 6.475 2
9046 KLHDC7A 1_13 0.9303 20.94 5.670e-05 4.124 1
9054 SPTY2D1 11_13 0.9096 33.33 8.823e-05 -5.557 1
1144 ASAP3 1_16 0.9084 33.50 8.855e-05 5.283 2
6097 ALLC 2_2 0.9041 27.81 7.317e-05 4.919 1
1320 CWF19L1 10_64 0.8853 35.76 9.213e-05 5.741 2
7350 BRI3 7_60 0.8734 28.79 7.319e-05 -5.140 2
11226 CLDN23 8_11 0.8662 23.95 6.038e-05 4.720 2
4680 TBC1D4 13_37 0.8636 20.07 5.043e-05 3.844 2
9827 PALM3 19_11 0.8572 20.18 5.033e-05 3.839 1
7919 PXK 3_40 0.8409 27.67 6.771e-05 -3.792 2
7992 TMEM150A 2_54 0.8393 21.22 5.184e-05 4.079 1
10459 PRMT6 1_66 0.8182 31.85 7.584e-05 -5.324 1
1846 CTSH 15_37 0.8061 20.48 4.805e-05 3.796 2Genes with largest effect sizes
#plot PIP vs effect size
plot(ctwas_gene_res$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 0.000000 6791.95 0.000e+00 -6.593 1
10399 LPA 6_104 0.000000 2114.15 0.000e+00 8.120 1
4433 PSRC1 1_67 1.000000 1652.10 4.808e-03 -41.687 1
5429 SYPL2 1_67 0.028366 647.10 5.342e-05 -25.890 2
NA.135 <NA> 6_104 0.000000 560.48 0.000e+00 -7.335 2
6966 ATXN7L2 1_67 0.033411 320.32 3.115e-05 -18.080 2
5375 GEMIN7 19_31 0.000000 276.41 0.000e+00 14.093 2
4315 ANGPTL3 1_39 0.992947 248.11 7.170e-04 16.132 1
NA.181 <NA> 8_83 0.008164 241.66 5.742e-06 14.404 1
NA.407 <NA> 1_121 0.999476 202.13 5.879e-04 -15.108 1
2454 ST3GAL4 11_77 1.000000 172.26 5.013e-04 13.376 2
781 PVR 19_31 0.000000 165.48 0.000e+00 -6.113 2
5988 FADS1 11_34 0.999902 163.14 4.747e-04 12.926 2
11327 HPR 16_38 1.000000 160.58 4.673e-04 -17.963 2
4047 NECTIN2 19_31 0.000000 108.03 0.000e+00 6.273 2
2092 SP4 7_19 0.981672 101.51 2.900e-04 10.693 1
9251 ZNF329 19_39 0.060635 97.71 1.724e-05 9.498 2
9910 RHCE 1_18 0.169841 97.63 4.826e-05 10.120 2
9428 TMEM50A 1_18 0.127944 97.18 3.619e-05 10.082 1
9438 EMILIN3 20_25 0.044392 94.40 1.220e-05 9.589 2Genes with highest PVE
#genes with 20 highest pve
head(ctwas_gene_res[order(-ctwas_gene_res$PVE),report_cols],20) genename region_tag susie_pip mu2 PVE z num_eqtl
4433 PSRC1 1_67 1.0000 1652.10 4.808e-03 -41.687 1
4315 ANGPTL3 1_39 0.9929 248.11 7.170e-04 16.132 1
NA.407 <NA> 1_121 0.9995 202.13 5.879e-04 -15.108 1
2454 ST3GAL4 11_77 1.0000 172.26 5.013e-04 13.376 2
5988 FADS1 11_34 0.9999 163.14 4.747e-04 12.926 2
11327 HPR 16_38 1.0000 160.58 4.673e-04 -17.963 2
2092 SP4 7_19 0.9817 101.51 2.900e-04 10.693 1
6090 CSNK1G3 5_75 0.9830 83.47 2.388e-04 9.116 1
8523 TNKS 8_12 0.9942 74.80 2.164e-04 11.039 2
10612 TRIM39 6_24 0.9990 70.98 2.064e-04 8.840 3
9365 GAS6 13_62 0.9927 70.41 2.034e-04 -8.924 1
3720 INSIG2 2_69 1.0000 68.08 1.981e-04 -8.983 3
1597 PLTP 20_28 0.9940 60.45 1.749e-04 -5.732 1
6774 PKN3 9_66 0.9504 47.07 1.302e-04 -6.621 1
5542 CNIH4 1_114 0.9931 40.46 1.170e-04 6.146 2
1009 GSK3B 3_74 0.9351 42.24 1.149e-04 6.475 2
10708 NYNRIN 14_3 0.7674 47.44 1.060e-04 7.010 3
11257 CYP2A6 19_28 0.9842 32.38 9.274e-05 5.407 1
3754 RRBP1 20_13 0.9924 32.02 9.247e-05 7.008 2
1114 SRRT 7_62 0.9732 32.63 9.241e-05 5.425 2Genes with largest z scores
#genes with 20 largest z scores
head(ctwas_gene_res[order(-abs(ctwas_gene_res$z)),report_cols],20) genename region_tag susie_pip mu2 PVE z num_eqtl
4433 PSRC1 1_67 1.000000 1652.10 4.808e-03 -41.687 1
5429 SYPL2 1_67 0.028366 647.10 5.342e-05 -25.890 2
6966 ATXN7L2 1_67 0.033411 320.32 3.115e-05 -18.080 2
11327 HPR 16_38 1.000000 160.58 4.673e-04 -17.963 2
4315 ANGPTL3 1_39 0.992947 248.11 7.170e-04 16.132 1
NA.407 <NA> 1_121 0.999476 202.13 5.879e-04 -15.108 1
NA.181 <NA> 8_83 0.008164 241.66 5.742e-06 14.404 1
5375 GEMIN7 19_31 0.000000 276.41 0.000e+00 14.093 2
2454 ST3GAL4 11_77 1.000000 172.26 5.013e-04 13.376 2
5988 FADS1 11_34 0.999902 163.14 4.747e-04 12.926 2
8523 TNKS 8_12 0.994247 74.80 2.164e-04 11.039 2
2092 SP4 7_19 0.981672 101.51 2.900e-04 10.693 1
9910 RHCE 1_18 0.169841 97.63 4.826e-05 10.120 2
9428 TMEM50A 1_18 0.127944 97.18 3.619e-05 10.082 1
2309 KPNB1 17_27 0.177130 93.33 4.811e-05 -9.790 2
9438 EMILIN3 20_25 0.044392 94.40 1.220e-05 9.589 2
9251 ZNF329 19_39 0.060635 97.71 1.724e-05 9.498 2
10475 TBKBP1 17_27 0.038167 87.99 9.774e-06 -9.319 2
9718 CEACAM19 19_31 0.000000 60.43 0.000e+00 -9.294 2
6090 CSNK1G3 5_75 0.983020 83.47 2.388e-04 9.116 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$z) > sig_thresh)[1] 113#proportion of significant z scores
mean(abs(ctwas_gene_res$z) > sig_thresh)[1] 0.0321#genes with most significant z scores
head(ctwas_gene_res[order(-abs(ctwas_gene_res$z)),report_cols],20) genename region_tag susie_pip mu2 PVE z num_eqtl
4433 PSRC1 1_67 1.000000 1652.10 4.808e-03 -41.687 1
5429 SYPL2 1_67 0.028366 647.10 5.342e-05 -25.890 2
6966 ATXN7L2 1_67 0.033411 320.32 3.115e-05 -18.080 2
11327 HPR 16_38 1.000000 160.58 4.673e-04 -17.963 2
4315 ANGPTL3 1_39 0.992947 248.11 7.170e-04 16.132 1
NA.407 <NA> 1_121 0.999476 202.13 5.879e-04 -15.108 1
NA.181 <NA> 8_83 0.008164 241.66 5.742e-06 14.404 1
5375 GEMIN7 19_31 0.000000 276.41 0.000e+00 14.093 2
2454 ST3GAL4 11_77 1.000000 172.26 5.013e-04 13.376 2
5988 FADS1 11_34 0.999902 163.14 4.747e-04 12.926 2
8523 TNKS 8_12 0.994247 74.80 2.164e-04 11.039 2
2092 SP4 7_19 0.981672 101.51 2.900e-04 10.693 1
9910 RHCE 1_18 0.169841 97.63 4.826e-05 10.120 2
9428 TMEM50A 1_18 0.127944 97.18 3.619e-05 10.082 1
2309 KPNB1 17_27 0.177130 93.33 4.811e-05 -9.790 2
9438 EMILIN3 20_25 0.044392 94.40 1.220e-05 9.589 2
9251 ZNF329 19_39 0.060635 97.71 1.724e-05 9.498 2
10475 TBKBP1 17_27 0.038167 87.99 9.774e-06 -9.319 2
9718 CEACAM19 19_31 0.000000 60.43 0.000e+00 -9.294 2
6090 CSNK1G3 5_75 0.983020 83.47 2.388e-04 9.116 1SNPs with highest PIPs
#snps with PIP>0.8 or 20 highest PIPs
head(ctwas_snp_res[order(-ctwas_snp_res$susie_pip),report_cols_snps],
max(sum(ctwas_snp_res$susie_pip>0.8), 20)) id region_tag susie_pip mu2 PVE z
14656 rs2495502 1_34 1.0000 305.87 8.901e-04 6.2922
69603 rs1042034 2_13 1.0000 238.93 6.953e-04 16.5730
69609 rs934197 2_13 1.0000 414.85 1.207e-03 33.0609
71339 rs780093 2_16 1.0000 169.08 4.920e-04 -14.1426
366947 rs12208357 6_103 1.0000 246.37 7.170e-04 12.2823
367050 rs60425481 6_104 1.0000 37673.16 1.096e-01 -7.1125
755541 rs113408695 17_39 1.0000 147.08 4.280e-04 12.7688
789399 rs73013176 19_9 1.0000 242.04 7.044e-04 -16.2327
799236 rs62117204 19_31 1.0000 825.94 2.404e-03 -44.6722
799254 rs111794050 19_31 1.0000 773.68 2.252e-03 -33.5996
799287 rs814573 19_31 1.0000 2239.73 6.518e-03 55.5379
799289 rs113345881 19_31 1.0000 783.78 2.281e-03 -34.3186
799292 rs12721109 19_31 1.0000 1359.81 3.957e-03 -46.3258
791930 rs3794991 19_15 1.0000 441.36 1.284e-03 -21.4921
755567 rs8070232 17_39 1.0000 154.27 4.490e-04 -8.0915
69554 rs11679386 2_12 1.0000 134.22 3.906e-04 11.9094
69689 rs1848922 2_13 1.0000 232.19 6.757e-04 25.4123
69612 rs548145 2_13 1.0000 667.51 1.943e-03 33.0860
493942 rs2437818 9_53 1.0000 70.49 2.051e-04 6.3340
502159 rs115478735 9_70 1.0000 309.16 8.997e-04 19.0118
1077630 rs1800961 20_28 1.0000 72.87 2.121e-04 -8.8970
799627 rs150262789 19_32 1.0000 78.48 2.284e-04 -10.8985
754625 rs1801689 17_38 1.0000 81.36 2.368e-04 9.3964
798950 rs73036721 19_30 1.0000 58.35 1.698e-04 -7.7879
441359 rs4738679 8_45 1.0000 108.88 3.169e-04 -11.6999
274124 rs1499279 5_30 1.0000 62.33 1.814e-04 -8.3746
77404 rs72800939 2_28 1.0000 56.23 1.636e-04 -7.8457
789437 rs137992968 19_9 1.0000 115.08 3.349e-04 -10.7526
14667 rs10888896 1_34 1.0000 135.17 3.934e-04 11.8938
7471 rs79598313 1_18 1.0000 47.06 1.369e-04 7.0246
461020 rs13252684 8_83 1.0000 230.52 6.708e-04 11.9644
439964 rs140753685 8_42 1.0000 55.62 1.619e-04 7.7992
798995 rs62115478 19_30 1.0000 183.37 5.336e-04 -14.3262
54531 rs2807848 1_112 1.0000 55.51 1.616e-04 -7.8828
1052221 rs9302635 16_38 1.0000 167.35 4.870e-04 -13.8393
14626 rs11580527 1_34 1.0000 88.74 2.583e-04 -11.1672
14674 rs471705 1_34 1.0000 211.19 6.146e-04 16.2630
348384 rs9496567 6_67 1.0000 39.03 1.136e-04 -6.3402
319169 rs11376017 6_13 0.9999 65.73 1.913e-04 -8.5079
791961 rs113619686 19_15 0.9999 57.37 1.669e-04 0.5939
789463 rs4804149 19_10 0.9999 46.38 1.350e-04 6.5194
77268 rs139029940 2_27 0.9997 39.25 1.142e-04 6.8150
367138 rs374071816 6_104 0.9996 6963.72 2.026e-02 16.2541
789428 rs1569372 19_9 0.9994 281.19 8.178e-04 10.0055
539902 rs17875416 10_71 0.9993 37.97 1.104e-04 -6.2663
323255 rs454182 6_22 0.9993 36.04 1.048e-04 4.7791
789516 rs322144 19_10 0.9992 57.41 1.669e-04 3.9466
605886 rs7397189 12_36 0.9991 34.33 9.982e-05 -5.7710
493915 rs2297400 9_53 0.9989 41.09 1.195e-04 6.6057
789423 rs3745677 19_9 0.9988 91.51 2.660e-04 9.3358
789420 rs147985405 19_9 0.9987 2298.38 6.680e-03 -48.9352
791570 rs2302209 19_14 0.9982 43.16 1.254e-04 6.6360
429691 rs1495743 8_20 0.9978 40.93 1.189e-04 -6.5160
280576 rs7701166 5_45 0.9971 33.67 9.771e-05 -2.4848
734645 rs2255451 16_48 0.9960 37.96 1.100e-04 -6.3628
582737 rs3135506 11_70 0.9957 148.12 4.292e-04 12.3730
582742 rs75542613 11_70 0.9956 35.81 1.038e-04 -6.5344
441327 rs56386732 8_45 0.9954 34.58 1.002e-04 -7.0123
814738 rs76981217 20_24 0.9953 35.33 1.023e-04 7.6925
323692 rs3130253 6_23 0.9942 29.84 8.632e-05 5.6415
621878 rs653178 12_67 0.9927 94.27 2.723e-04 11.0501
610252 rs148481241 12_44 0.9919 27.45 7.924e-05 5.0955
387191 rs217396 7_32 0.9914 68.19 1.968e-04 -9.4286
280517 rs10062361 5_45 0.9877 205.81 5.916e-04 20.3206
138652 rs709149 3_9 0.9857 35.96 1.032e-04 -6.7820
729318 rs4396539 16_37 0.9834 27.34 7.826e-05 -5.2329
145662 rs9834932 3_24 0.9807 65.78 1.878e-04 -8.4816
814689 rs6029132 20_24 0.9801 39.31 1.121e-04 -6.7625
625967 rs11057830 12_76 0.9792 25.82 7.357e-05 4.9296
814742 rs73124945 20_24 0.9782 32.16 9.156e-05 -7.7754
403009 rs3197597 7_61 0.9762 28.92 8.215e-05 -5.0452
461009 rs79658059 8_83 0.9711 273.10 7.718e-04 -16.0220
243931 rs114756490 4_100 0.9707 26.19 7.400e-05 4.9889
387241 rs141379002 7_33 0.9696 25.62 7.230e-05 4.8970
799610 rs34942359 19_32 0.9655 62.49 1.756e-04 -7.0096
822743 rs62219001 21_2 0.9607 26.10 7.297e-05 -4.9484
221202 rs1458038 4_54 0.9604 52.56 1.469e-04 -7.4179
476267 rs1556516 9_16 0.9570 73.35 2.043e-04 -8.9921
591369 rs11048034 12_9 0.9550 35.79 9.947e-05 6.1337
758700 rs4969183 17_44 0.9529 48.75 1.352e-04 7.1693
469072 rs7024888 9_3 0.9507 25.98 7.187e-05 -5.0558
624832 rs1169300 12_74 0.9503 68.16 1.885e-04 8.6855
322716 rs75080831 6_19 0.9460 56.94 1.568e-04 -7.9067
77284 rs4076834 2_27 0.9336 428.47 1.164e-03 -20.1086
566366 rs6591179 11_36 0.9327 24.99 6.784e-05 4.8933
619971 rs1196760 12_63 0.9310 25.89 7.014e-05 -4.8667
77281 rs13430143 2_27 0.9274 78.02 2.106e-04 -3.3445
351120 rs12199109 6_73 0.9238 24.76 6.657e-05 4.8570
1054611 rs2908806 17_7 0.9222 37.24 9.996e-05 -6.0264
192827 rs5855544 3_120 0.9199 23.87 6.390e-05 -4.5937
69606 rs78610189 2_13 0.9172 59.43 1.586e-04 -8.3855
366941 rs9456502 6_103 0.9146 33.18 8.833e-05 5.9640
745084 rs117859452 17_17 0.9081 24.26 6.411e-05 -3.8517
14657 rs1887552 1_34 0.9062 349.25 9.211e-04 -9.8686
799527 rs377297589 19_32 0.9008 50.78 1.331e-04 -6.7865
194614 rs36205397 4_4 0.8982 38.68 1.011e-04 6.1594
725426 rs821840 16_31 0.8959 163.96 4.275e-04 -13.4753
507109 rs10905277 10_8 0.8956 27.89 7.270e-05 5.1258
806012 rs74273659 20_5 0.8953 24.51 6.386e-05 4.6468
539613 rs12244851 10_70 0.8912 36.60 9.492e-05 -4.8831
803822 rs34003091 19_39 0.8891 103.45 2.677e-04 -10.4237
789504 rs322125 19_10 0.8883 102.55 2.651e-04 -7.4704
196839 rs2002574 4_10 0.8837 24.56 6.315e-05 -4.5583
744993 rs3032928 17_17 0.8829 33.85 8.698e-05 6.1119
493935 rs2777788 9_53 0.8791 58.23 1.490e-04 -5.7370
579006 rs201912654 11_59 0.8724 40.09 1.018e-04 -6.3056
634854 rs1012130 13_10 0.8719 39.28 9.967e-05 -2.7810
323663 rs28986304 6_23 0.8676 41.74 1.054e-04 7.3825
818241 rs10641149 20_32 0.8666 27.13 6.842e-05 5.0758
829984 rs2835302 21_17 0.8646 25.71 6.469e-05 -4.6537
120749 rs7569317 2_120 0.8576 43.89 1.095e-04 7.9007
69406 rs6531234 2_12 0.8531 42.19 1.047e-04 -7.1708
484253 rs11144506 9_35 0.8502 26.96 6.671e-05 5.0427
789473 rs58495388 19_10 0.8495 33.86 8.371e-05 5.5313
814707 rs6102034 20_24 0.8438 96.82 2.377e-04 -11.1900
280540 rs3843482 5_45 0.8401 402.71 9.845e-04 25.0344
357323 rs9321207 6_86 0.8319 30.70 7.433e-05 5.4016
813483 rs11167269 20_21 0.8302 57.10 1.380e-04 -7.7950
750212 rs4793601 17_28 0.8237 30.61 7.338e-05 -6.2095
755552 rs9303012 17_39 0.8172 146.84 3.492e-04 2.2591
534403 rs10882161 10_59 0.8167 29.87 7.100e-05 -5.4756
634846 rs1799955 13_10 0.8162 70.55 1.676e-04 -6.6936SNPs 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
367046 rs3106169 6_104 6.281e-01 37722 6.895e-02 11.139
367047 rs3127598 6_104 4.719e-01 37722 5.180e-02 11.135
367055 rs3106167 6_104 4.793e-01 37721 5.261e-02 11.136
367039 rs11755965 6_104 1.129e-01 37711 1.239e-02 11.140
367050 rs60425481 6_104 1.000e+00 37673 1.096e-01 -7.113
367030 rs12194962 6_104 1.571e-07 37631 1.720e-08 11.106
367048 rs3127597 6_104 2.003e-08 37606 2.192e-09 11.145
367009 rs3119311 6_104 0.000e+00 27265 0.000e+00 8.031
367003 rs3127579 6_104 0.000e+00 19863 0.000e+00 7.568
366997 rs10945658 6_104 0.000e+00 17395 0.000e+00 8.309
366992 rs3103352 6_104 0.000e+00 17354 0.000e+00 8.522
366996 rs3119308 6_104 0.000e+00 17352 0.000e+00 8.274
366988 rs3101821 6_104 0.000e+00 17294 0.000e+00 8.528
366994 rs12205178 6_104 0.000e+00 17254 0.000e+00 8.297
366986 rs148015788 6_104 0.000e+00 17037 0.000e+00 8.351
367097 rs3124784 6_104 0.000e+00 14303 0.000e+00 9.680
367098 rs3127596 6_104 0.000e+00 12984 0.000e+00 9.556
367091 rs3127599 6_104 0.000e+00 12917 0.000e+00 9.259
367061 rs2481030 6_104 0.000e+00 12353 0.000e+00 4.811
367026 rs2504949 6_104 0.000e+00 10166 0.000e+00 2.937
367079 rs388170 6_104 0.000e+00 9414 0.000e+00 3.833
367001 rs316013 6_104 0.000e+00 9022 0.000e+00 -3.002
367002 rs316012 6_104 0.000e+00 8914 0.000e+00 -3.074
367082 rs9355288 6_104 0.000e+00 8736 0.000e+00 6.319
366990 rs610206 6_104 0.000e+00 8238 0.000e+00 -2.944
366991 rs595374 6_104 0.000e+00 8222 0.000e+00 -2.921
366998 rs315995 6_104 0.000e+00 8024 0.000e+00 -3.207
366995 rs543435 6_104 0.000e+00 7994 0.000e+00 -3.250
367044 rs452867 6_104 0.000e+00 7570 0.000e+00 -7.124
367053 rs367334 6_104 0.000e+00 7564 0.000e+00 -7.106
367041 rs589931 6_104 0.000e+00 7563 0.000e+00 -7.116
367042 rs600584 6_104 0.000e+00 7563 0.000e+00 -7.113
367043 rs434953 6_104 0.000e+00 7563 0.000e+00 -7.111
367049 rs380498 6_104 0.000e+00 7563 0.000e+00 -7.115
367017 rs3119312 6_104 0.000e+00 7226 0.000e+00 3.771
367138 rs374071816 6_104 9.996e-01 6964 2.026e-02 16.254
367076 rs2872317 6_104 0.000e+00 6656 0.000e+00 6.746
367073 rs2313453 6_104 0.000e+00 6651 0.000e+00 6.718
367143 rs4252185 6_104 4.313e-04 6425 8.065e-06 15.878
367064 rs146184004 6_104 0.000e+00 6335 0.000e+00 6.534
367067 rs624319 6_104 0.000e+00 6260 0.000e+00 -6.291
367066 rs637614 6_104 0.000e+00 6252 0.000e+00 -6.362
367068 rs486339 6_104 0.000e+00 6209 0.000e+00 -6.311
367013 rs316036 6_104 0.000e+00 6097 0.000e+00 -7.009
367065 rs555754 6_104 0.000e+00 6055 0.000e+00 -6.593
367144 rs12212146 6_104 0.000e+00 4816 0.000e+00 -2.410
367011 rs582280 6_104 0.000e+00 4671 0.000e+00 2.635
367010 rs497039 6_104 0.000e+00 4670 0.000e+00 2.634
367094 rs9346818 6_104 0.000e+00 3837 0.000e+00 7.950
367197 rs1247539 6_104 0.000e+00 3790 0.000e+00 -4.294SNPs 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
367050 rs60425481 6_104 1.0000 37673.16 0.1096358 -7.113
367046 rs3106169 6_104 0.6281 37721.87 0.0689541 11.139
367055 rs3106167 6_104 0.4793 37721.42 0.0526133 11.136
367047 rs3127598 6_104 0.4719 37721.52 0.0518047 11.135
367138 rs374071816 6_104 0.9996 6963.72 0.0202570 16.254
367039 rs11755965 6_104 0.1129 37710.55 0.0123867 11.140
789420 rs147985405 19_9 0.9987 2298.38 0.0066798 -48.935
799287 rs814573 19_31 1.0000 2239.73 0.0065180 55.538
799292 rs12721109 19_31 1.0000 1359.81 0.0039573 -46.326
799236 rs62117204 19_31 1.0000 825.94 0.0024036 -44.672
799289 rs113345881 19_31 1.0000 783.78 0.0022809 -34.319
799254 rs111794050 19_31 1.0000 773.68 0.0022516 -33.600
69612 rs548145 2_13 1.0000 667.51 0.0019426 33.086
791930 rs3794991 19_15 1.0000 441.36 0.0012844 -21.492
69609 rs934197 2_13 1.0000 414.85 0.0012073 33.061
77284 rs4076834 2_27 0.9336 428.47 0.0011641 -20.109
280540 rs3843482 5_45 0.8401 402.71 0.0009845 25.034
14657 rs1887552 1_34 0.9062 349.25 0.0009211 -9.869
502159 rs115478735 9_70 1.0000 309.16 0.0008997 19.012
14656 rs2495502 1_34 1.0000 305.87 0.0008901 6.292
789428 rs1569372 19_9 0.9994 281.19 0.0008178 10.006
461009 rs79658059 8_83 0.9711 273.10 0.0007718 -16.022
366947 rs12208357 6_103 1.0000 246.37 0.0007170 12.282
789399 rs73013176 19_9 1.0000 242.04 0.0007044 -16.233
69603 rs1042034 2_13 1.0000 238.93 0.0006953 16.573
69689 rs1848922 2_13 1.0000 232.19 0.0006757 25.412
461020 rs13252684 8_83 1.0000 230.52 0.0006708 11.964
14674 rs471705 1_34 1.0000 211.19 0.0006146 16.263
280517 rs10062361 5_45 0.9877 205.81 0.0005916 20.321
798995 rs62115478 19_30 1.0000 183.37 0.0005336 -14.326
71339 rs780093 2_16 1.0000 169.08 0.0004920 -14.143
1052221 rs9302635 16_38 1.0000 167.35 0.0004870 -13.839
755567 rs8070232 17_39 1.0000 154.27 0.0004490 -8.091
366961 rs3818678 6_103 0.7673 199.28 0.0004450 -9.948
582737 rs3135506 11_70 0.9957 148.12 0.0004292 12.373
755541 rs113408695 17_39 1.0000 147.08 0.0004280 12.769
725426 rs821840 16_31 0.8959 163.96 0.0004275 -13.475
14667 rs10888896 1_34 1.0000 135.17 0.0003934 11.894
69554 rs11679386 2_12 1.0000 134.22 0.0003906 11.909
755552 rs9303012 17_39 0.8172 146.84 0.0003492 2.259
305419 rs12657266 5_92 0.7541 158.13 0.0003470 13.895
789437 rs137992968 19_9 1.0000 115.08 0.0003349 -10.753
1052033 rs77303550 16_38 0.6757 163.45 0.0003214 -13.733
441359 rs4738679 8_45 1.0000 108.88 0.0003169 -11.700
461008 rs2980875 8_83 0.5445 185.03 0.0002932 -22.102
621878 rs653178 12_67 0.9927 94.27 0.0002723 11.050
803822 rs34003091 19_39 0.8891 103.45 0.0002677 -10.424
789423 rs3745677 19_9 0.9988 91.51 0.0002660 9.336
789504 rs322125 19_10 0.8883 102.55 0.0002651 -7.470
14626 rs11580527 1_34 1.0000 88.74 0.0002583 -11.167SNPs 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
799287 rs814573 19_31 1.000e+00 2239.7 6.518e-03 55.54
789420 rs147985405 19_9 9.987e-01 2298.4 6.680e-03 -48.94
789415 rs73015020 19_9 7.913e-04 2286.0 5.264e-06 -48.80
789413 rs138175288 19_9 3.689e-04 2284.2 2.452e-06 -48.78
789414 rs138294113 19_9 8.891e-05 2280.4 5.901e-07 -48.75
789416 rs77140532 19_9 5.376e-05 2280.8 3.568e-07 -48.74
789417 rs112552009 19_9 2.699e-05 2276.9 1.788e-07 -48.71
789418 rs10412048 19_9 1.083e-05 2277.5 7.179e-08 -48.70
789412 rs55997232 19_9 2.344e-09 2257.2 1.540e-11 -48.52
799292 rs12721109 19_31 1.000e+00 1359.8 3.957e-03 -46.33
799236 rs62117204 19_31 1.000e+00 825.9 2.404e-03 -44.67
799223 rs1551891 19_31 0.000e+00 499.4 0.000e+00 -42.27
870728 rs12740374 1_67 7.500e-04 1482.3 3.235e-06 -41.79
870724 rs7528419 1_67 7.548e-04 1478.4 3.248e-06 -41.74
870735 rs646776 1_67 6.337e-04 1476.8 2.724e-06 41.73
870734 rs629301 1_67 5.825e-04 1473.0 2.497e-06 41.69
870746 rs583104 1_67 6.366e-04 1431.8 2.653e-06 41.09
870749 rs4970836 1_67 6.239e-04 1428.8 2.594e-06 41.05
870751 rs1277930 1_67 6.381e-04 1424.0 2.645e-06 40.98
870752 rs599839 1_67 6.588e-04 1423.1 2.728e-06 40.96
789421 rs17248769 19_9 6.725e-08 1730.4 3.387e-10 -40.84
789422 rs2228671 19_9 4.781e-08 1719.4 2.392e-10 -40.70
870732 rs3832016 1_67 4.279e-04 1382.4 1.721e-06 40.40
870729 rs660240 1_67 4.264e-04 1375.1 1.706e-06 40.29
870747 rs602633 1_67 4.856e-04 1353.7 1.913e-06 39.96
789411 rs9305020 19_9 2.909e-14 1313.8 1.112e-16 -34.84
799283 rs405509 19_31 0.000e+00 975.9 0.000e+00 -34.64
870715 rs4970834 1_67 9.850e-04 1021.7 2.929e-06 -34.62
799289 rs113345881 19_31 1.000e+00 783.8 2.281e-03 -34.32
799207 rs62120566 19_31 0.000e+00 1339.0 0.000e+00 -33.74
799254 rs111794050 19_31 1.000e+00 773.7 2.252e-03 -33.60
69612 rs548145 2_13 1.000e+00 667.5 1.943e-03 33.09
799260 rs4802238 19_31 0.000e+00 979.6 0.000e+00 33.08
69609 rs934197 2_13 1.000e+00 414.8 1.207e-03 33.06
799201 rs188099946 19_31 0.000e+00 1283.4 0.000e+00 -33.04
799271 rs2972559 19_31 0.000e+00 1310.8 0.000e+00 32.29
799195 rs201314191 19_31 0.000e+00 1190.0 0.000e+00 -32.07
870736 rs3902354 1_67 4.819e-04 871.8 1.223e-06 32.00
870725 rs11102967 1_67 4.843e-04 868.2 1.224e-06 31.94
870750 rs4970837 1_67 5.616e-04 864.7 1.413e-06 31.86
799262 rs56394238 19_31 0.000e+00 973.2 0.000e+00 31.55
799239 rs2965169 19_31 0.000e+00 359.4 0.000e+00 -31.38
799263 rs3021439 19_31 0.000e+00 866.0 0.000e+00 31.05
870720 rs611917 1_67 4.507e-04 817.3 1.072e-06 -30.98
69639 rs12997242 2_13 2.334e-11 382.1 2.596e-14 30.82
799270 rs12162222 19_31 0.000e+00 1122.3 0.000e+00 30.50
69613 rs478588 2_13 7.657e-11 615.3 1.371e-13 30.49
799200 rs62119327 19_31 0.000e+00 1047.7 0.000e+00 -30.42
69614 rs56350433 2_13 3.217e-12 350.8 3.285e-15 30.23
69619 rs56079819 2_13 3.223e-12 350.0 3.283e-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