T2D - Adipose Subcutaneous
sheng Qian
2021-2-6
Last updated: 2022-02-26
Checks: 6 1
Knit directory: cTWAS_analysis/
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| html | 91f38fa | sq-96 | 2022-02-13 | Build site. |
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Weight QC
[1] 8591
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
874 679 536 364 458 498 421 323 333 362 534 523 182 297 322 342 434 142 429 246
21 22
102 190 [1] 4545[1] 0.529042Load ctwas results
Check convergence of parameters
********************************************************Note: As of version 1.0.0, cowplot does not change the default ggplot2 theme anymore. To recover the previous behavior, execute:
theme_set(theme_cowplot())********************************************************
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
gene snp
0.0164052744 0.0003491226 gene snp
9.541881 8.856665 [1] 62892[1] 8591 5017200 gene snp
0.02138286 0.24666880 [1] 0.097563 1.394008Genes with highest PIPs
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
genename region_tag susie_pip mu2 PVE z num_eqtl
7109 LONRF1 8_15 0.9929090 29.21253 0.0004611935 -5.424976 2
5112 P2RX4 12_74 0.9614949 25.94139 0.0003965927 5.081395 1
250 ANGEL1 14_36 0.9577010 22.67702 0.0003453190 4.529353 2
7272 KCNS2 8_68 0.9084550 26.21428 0.0003786570 -5.148148 1
7654 PTH1R 3_33 0.8979756 30.11423 0.0004299728 -5.646341 1
6918 ARL14EP 11_21 0.8714865 23.28173 0.0003226120 -4.877816 2
13239 N4BP2L2 13_11 0.8441484 24.33744 0.0003266617 -4.430380 1
10030 FAM89B 11_36 0.7961326 24.33365 0.0003080330 5.011364 1
8836 FAM234A 16_1 0.7887942 31.18972 0.0003911829 5.621053 1
11712 PARVA 11_9 0.7846449 20.35377 0.0002539351 -3.862069 1
7267 GDF6 8_67 0.7821456 21.36036 0.0002656444 -4.371795 1
3924 SEPT7 7_26 0.7750777 20.71351 0.0002552722 -4.166667 1
3988 ZC3H13 13_19 0.7732369 20.55708 0.0002527427 4.310345 1
2323 DNASE2 19_10 0.7718480 18.79133 0.0002306184 -3.744186 1
4009 KBTBD4 11_29 0.7473759 26.46156 0.0003144555 -5.097561 1
3282 GRB14 2_100 0.7261964 21.31644 0.0002461349 4.744898 1
11149 SLIT1 10_62 0.7054051 24.44621 0.0002741919 4.797347 2
7490 UBE2Z 17_28 0.7027425 47.07794 0.0005260394 -7.392405 1
6245 MRPS5 2_57 0.6981455 19.67432 0.0002183988 -3.809979 2
10469 TMEM132E 17_20 0.6953548 21.32974 0.0002358287 -3.692999 2Genes with largest effect sizes
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
genename region_tag susie_pip mu2 PVE z
7048 JAZF1 7_23 0.010489657 138.57315 2.311240e-05 -12.730769
14285 RP11-395N3.2 2_133 0.035388941 109.23628 6.146658e-05 -11.370370
356 ANK1 8_36 0.040525872 59.39273 3.827104e-05 8.666667
6954 ZFP36L2 2_27 0.039417323 55.29285 3.465458e-05 8.376923
2723 WFS1 4_7 0.029567029 53.22895 2.502420e-05 10.641975
8537 C2 6_26 0.219640555 52.12414 1.820355e-04 7.148936
11174 KCNJ11 11_12 0.022352569 49.76935 1.768862e-05 7.230769
11270 NCR3LG1 11_12 0.022725263 49.30958 1.781742e-05 -7.168932
14659 LINC01126 2_27 0.049133590 47.84997 3.738219e-05 -7.520384
1417 PABPC4 1_24 0.208389179 47.84681 1.585378e-04 -7.054348
7490 UBE2Z 17_28 0.702742531 47.07794 5.260394e-04 -7.392405
3368 THADA 2_27 0.037435740 45.74582 2.722967e-05 7.450450
943 ZZEF1 17_4 0.090686616 43.96105 6.338928e-05 6.916667
10282 ZNF664 12_75 0.315660986 43.32163 2.174354e-04 -6.452055
7491 SNF8 17_28 0.064661984 43.16571 4.438053e-05 6.300000
10726 BMP8A 1_24 0.090840980 42.58988 6.151667e-05 6.868132
6449 CDKAL1 6_15 0.003751902 40.70165 2.428108e-06 -8.191860
10555 UBE2E2 3_17 0.498580721 39.49123 3.130695e-04 6.080882
3647 CCDC92 12_75 0.108517987 38.03243 6.562365e-05 -5.498713
13467 RP11-419C23.1 8_33 0.506566550 37.39164 3.011727e-04 -6.316832
num_eqtl
7048 1
14285 1
356 1
6954 1
2723 1
8537 1
11174 1
11270 2
14659 2
1417 1
7490 1
3368 1
943 1
10282 1
7491 1
10726 1
6449 1
10555 1
3647 5
13467 1Genes with highest PVE
genename region_tag susie_pip mu2 PVE z
7490 UBE2Z 17_28 0.7027425 47.07794 0.0005260394 -7.392405
7109 LONRF1 8_15 0.9929090 29.21253 0.0004611935 -5.424976
7654 PTH1R 3_33 0.8979756 30.11423 0.0004299728 -5.646341
5112 P2RX4 12_74 0.9614949 25.94139 0.0003965927 5.081395
8836 FAM234A 16_1 0.7887942 31.18972 0.0003911829 5.621053
7272 KCNS2 8_68 0.9084550 26.21428 0.0003786570 -5.148148
250 ANGEL1 14_36 0.9577010 22.67702 0.0003453190 4.529353
13239 N4BP2L2 13_11 0.8441484 24.33744 0.0003266617 -4.430380
6918 ARL14EP 11_21 0.8714865 23.28173 0.0003226120 -4.877816
4009 KBTBD4 11_29 0.7473759 26.46156 0.0003144555 -5.097561
10555 UBE2E2 3_17 0.4985807 39.49123 0.0003130695 6.080882
10030 FAM89B 11_36 0.7961326 24.33365 0.0003080330 5.011364
13467 RP11-419C23.1 8_33 0.5065666 37.39164 0.0003011727 -6.316832
6645 CAMK2G 10_49 0.5494966 32.00592 0.0002796404 5.012658
11149 SLIT1 10_62 0.7054051 24.44621 0.0002741919 4.797347
7267 GDF6 8_67 0.7821456 21.36036 0.0002656444 -4.371795
3924 SEPT7 7_26 0.7750777 20.71351 0.0002552722 -4.166667
11712 PARVA 11_9 0.7846449 20.35377 0.0002539351 -3.862069
3988 ZC3H13 13_19 0.7732369 20.55708 0.0002527427 4.310345
3282 GRB14 2_100 0.7261964 21.31644 0.0002461349 4.744898
num_eqtl
7490 1
7109 2
7654 1
5112 1
8836 1
7272 1
250 2
13239 1
6918 2
4009 1
10555 1
10030 1
13467 1
6645 1
11149 2
7267 1
3924 1
11712 1
3988 1
3282 1Genes with largest z scores
genename region_tag susie_pip mu2 PVE z
7048 JAZF1 7_23 0.010489657 138.57315 2.311240e-05 -12.730769
14285 RP11-395N3.2 2_133 0.035388941 109.23628 6.146658e-05 -11.370370
2723 WFS1 4_7 0.029567029 53.22895 2.502420e-05 10.641975
356 ANK1 8_36 0.040525872 59.39273 3.827104e-05 8.666667
6954 ZFP36L2 2_27 0.039417323 55.29285 3.465458e-05 8.376923
6449 CDKAL1 6_15 0.003751902 40.70165 2.428108e-06 -8.191860
14659 LINC01126 2_27 0.049133590 47.84997 3.738219e-05 -7.520384
3368 THADA 2_27 0.037435740 45.74582 2.722967e-05 7.450450
7490 UBE2Z 17_28 0.702742531 47.07794 5.260394e-04 -7.392405
11174 KCNJ11 11_12 0.022352569 49.76935 1.768862e-05 7.230769
11270 NCR3LG1 11_12 0.022725263 49.30958 1.781742e-05 -7.168932
8537 C2 6_26 0.219640555 52.12414 1.820355e-04 7.148936
1417 PABPC4 1_24 0.208389179 47.84681 1.585378e-04 -7.054348
943 ZZEF1 17_4 0.090686616 43.96105 6.338928e-05 6.916667
10726 BMP8A 1_24 0.090840980 42.58988 6.151667e-05 6.868132
10282 ZNF664 12_75 0.315660986 43.32163 2.174354e-04 -6.452055
12119 MICB 6_25 0.483137672 29.83545 2.291966e-04 6.443315
13467 RP11-419C23.1 8_33 0.506566550 37.39164 3.011727e-04 -6.316832
7491 SNF8 17_28 0.064661984 43.16571 4.438053e-05 6.300000
7368 AP3S2 15_41 0.392663862 36.07772 2.252499e-04 6.272710
num_eqtl
7048 1
14285 1
2723 1
356 1
6954 1
6449 1
14659 2
3368 1
7490 1
11174 1
11270 2
8537 1
1417 1
943 1
10726 1
10282 1
12119 3
13467 1
7491 1
7368 2Comparing z scores and PIPs
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
[1] 0.009079269 genename region_tag susie_pip mu2 PVE z
7048 JAZF1 7_23 0.010489657 138.57315 2.311240e-05 -12.730769
14285 RP11-395N3.2 2_133 0.035388941 109.23628 6.146658e-05 -11.370370
2723 WFS1 4_7 0.029567029 53.22895 2.502420e-05 10.641975
356 ANK1 8_36 0.040525872 59.39273 3.827104e-05 8.666667
6954 ZFP36L2 2_27 0.039417323 55.29285 3.465458e-05 8.376923
6449 CDKAL1 6_15 0.003751902 40.70165 2.428108e-06 -8.191860
14659 LINC01126 2_27 0.049133590 47.84997 3.738219e-05 -7.520384
3368 THADA 2_27 0.037435740 45.74582 2.722967e-05 7.450450
7490 UBE2Z 17_28 0.702742531 47.07794 5.260394e-04 -7.392405
11174 KCNJ11 11_12 0.022352569 49.76935 1.768862e-05 7.230769
11270 NCR3LG1 11_12 0.022725263 49.30958 1.781742e-05 -7.168932
8537 C2 6_26 0.219640555 52.12414 1.820355e-04 7.148936
1417 PABPC4 1_24 0.208389179 47.84681 1.585378e-04 -7.054348
943 ZZEF1 17_4 0.090686616 43.96105 6.338928e-05 6.916667
10726 BMP8A 1_24 0.090840980 42.58988 6.151667e-05 6.868132
10282 ZNF664 12_75 0.315660986 43.32163 2.174354e-04 -6.452055
12119 MICB 6_25 0.483137672 29.83545 2.291966e-04 6.443315
13467 RP11-419C23.1 8_33 0.506566550 37.39164 3.011727e-04 -6.316832
7491 SNF8 17_28 0.064661984 43.16571 4.438053e-05 6.300000
7368 AP3S2 15_41 0.392663862 36.07772 2.252499e-04 6.272710
num_eqtl
7048 1
14285 1
2723 1
356 1
6954 1
6449 1
14659 2
3368 1
7490 1
11174 1
11270 2
8537 1
1417 1
943 1
10726 1
10282 1
12119 3
13467 1
7491 1
7368 2Sensitivity, specificity and precision for silver standard genes
[1] 72[1] 25[1] 4.532824[1] 7[1] 78 genename region_tag susie_pip mu2 PVE z num_eqtl
13239 N4BP2L2 13_11 0.8441484 24.33744 0.0003266617 -4.430380 1
250 ANGEL1 14_36 0.9577010 22.67702 0.0003453190 4.529353 2 ctwas TWAS
0.00000000 0.02777778 ctwas TWAS
0.9991828 0.9911277 ctwas TWAS
0.00000000 0.02564103 
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.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] readxl_1.3.1 cowplot_1.0.0 ggplot2_3.3.5 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] tidyselect_1.1.1 xfun_0.29 purrr_0.3.4 colorspace_2.0-2
[5] vctrs_0.3.8 generics_0.1.1 htmltools_0.5.2 yaml_2.2.1
[9] utf8_1.2.2 blob_1.2.2 rlang_1.0.1 jquerylib_0.1.4
[13] later_0.8.0 pillar_1.6.4 glue_1.6.2 withr_2.4.3
[17] DBI_1.1.2 bit64_4.0.5 lifecycle_1.0.1 stringr_1.4.0
[21] cellranger_1.1.0 munsell_0.5.0 gtable_0.3.0 evaluate_0.14
[25] memoise_2.0.1 labeling_0.4.2 knitr_1.36 fastmap_1.1.0
[29] httpuv_1.5.1 fansi_1.0.2 highr_0.9 Rcpp_1.0.8
[33] promises_1.0.1 scales_1.1.1 cachem_1.0.6 farver_2.1.0
[37] fs_1.5.2 bit_4.0.4 digest_0.6.29 stringi_1.7.6
[41] dplyr_1.0.7 rprojroot_2.0.2 grid_3.6.1 cli_3.1.0
[45] tools_3.6.1 magrittr_2.0.2 tibble_3.1.6 RSQLite_2.2.8
[49] crayon_1.5.0 whisker_0.3-2 pkgconfig_2.0.3 ellipsis_0.3.2
[53] data.table_1.14.2 assertthat_0.2.1 rmarkdown_2.11 R6_2.5.1
[57] git2r_0.26.1 compiler_3.6.1