T2D - Adipose Visceral Omentum
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. |
| Rmd | eb13ecf | sq-96 | 2022-02-13 | update |
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Weight QC
[1] 8279
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
860 632 533 357 434 491 417 287 316 367 525 508 179 281 284 320 451 139 400 239
21 22
83 176 [1] 4625[1] 0.5586423Load 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
0.0185530132 0.0003497053 gene snp
7.211326 8.953709 [1] 62892[1] 8279 5017190 gene snp
0.01761214 0.24978730 [1] 0.102309 1.400366Genes with highest PIPs
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
genename region_tag susie_pip mu2 PVE z num_eqtl
8882 POLR2J3 7_63 0.9604481 25.73621 0.0003930277 4.987179 1
7980 LMOD1 1_102 0.9455781 24.42585 0.0003672414 -4.906667 1
249 ANGEL1 14_36 0.9355098 21.80009 0.0003242733 4.558286 2
3617 ARG1 6_87 0.9093784 29.86900 0.0004318868 -5.606383 1
1848 CTSZ 20_34 0.8804599 20.17505 0.0002824416 -3.895833 1
7655 PTH1R 3_33 0.8779571 28.46963 0.0003974292 -5.646341 1
3290 GRB14 2_100 0.8747366 25.00435 0.0003477743 5.163265 1
14287 RP5-899E9.1 7_49 0.8131882 19.91257 0.0002574678 -4.333333 1
4668 ZNF236 18_45 0.7874377 20.13940 0.0002521548 -4.378049 1
7322 NTAN1 16_15 0.7753888 19.37072 0.0002388196 4.191781 1
9579 DMRT2 9_1 0.7497494 19.40307 0.0002313082 -4.317647 1
10241 ZNF664 12_75 0.7398435 41.10919 0.0004835967 -6.452055 1
9990 SEC24C 10_49 0.7329619 26.90018 0.0003135026 -4.862500 1
2306 DNASE2 19_10 0.7295752 18.47136 0.0002142760 -3.744186 1
11753 TMEM229B 14_31 0.7256206 18.30602 0.0002112069 -3.658228 1
1508 CWF19L1 10_64 0.6961732 33.33104 0.0003689527 -5.810127 1
5258 C2orf49 2_62 0.6887055 26.87816 0.0002943322 5.234783 1
13192 LINC01184 5_78 0.6804573 18.63653 0.0002016372 3.793478 1
6264 MRPS5 2_57 0.6164002 20.19764 0.0001979557 -3.736842 1
6029 SCYL1 11_36 0.6145439 22.22566 0.0002171762 -4.813953 1Genes with largest effect sizes
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
genename region_tag susie_pip mu2 PVE z
7057 JAZF1 7_23 0.277121240 130.41581 5.746517e-04 -12.662338
2722 WFS1 4_7 0.158489875 64.77219 1.632280e-04 11.434211
3379 THADA 2_27 0.063977825 59.34224 6.036678e-05 8.666667
14565 LINC01126 2_27 0.050344112 52.17727 4.176713e-05 -8.376923
10525 UBE2E2 3_17 0.084142485 48.51436 6.490681e-05 7.166009
11136 KCNJ11 11_12 0.028462071 45.08258 2.040234e-05 7.075347
11227 NCR3LG1 11_12 0.035886976 44.07749 2.515118e-05 -6.854088
3273 NRBP1 2_16 0.057481036 43.85515 4.008204e-05 -6.625000
7493 UBE2Z 17_28 0.607571388 43.82484 4.233721e-04 -7.392405
3656 CCDC92 12_75 0.135611254 42.88152 9.246353e-05 -5.886761
1401 PABPC4 1_24 0.103951722 42.78419 7.071631e-05 -6.817204
7491 ATP5G1 17_28 0.090094897 41.34788 5.923222e-05 6.400000
10241 ZNF664 12_75 0.739843464 41.10919 4.835967e-04 -6.452055
1158 COBLL1 2_100 0.072550762 39.99019 4.613177e-05 -5.375000
12780 CYP21A2 6_26 0.055454852 39.91456 3.519456e-05 6.452632
7494 SNF8 17_28 0.077698290 39.44087 4.872620e-05 6.300000
9611 PEAK1 15_36 0.478499702 39.01754 2.968563e-04 -6.885057
6467 CDKAL1 6_15 0.004169188 37.80537 2.506165e-06 -8.191860
7378 AP3S2 15_41 0.369115688 36.18157 2.123511e-04 6.356322
5126 P2RX4 12_74 0.263754799 35.41665 1.485294e-04 4.096154
num_eqtl
7057 1
2722 1
3379 1
14565 1
10525 2
11136 2
11227 2
3273 1
7493 1
3656 2
1401 1
7491 1
10241 1
1158 1
12780 1
7494 1
9611 1
6467 1
7378 1
5126 1Genes with highest PVE
genename region_tag susie_pip mu2 PVE z
7057 JAZF1 7_23 0.2771212 130.41581 0.0005746517 -12.662338
10241 ZNF664 12_75 0.7398435 41.10919 0.0004835967 -6.452055
3617 ARG1 6_87 0.9093784 29.86900 0.0004318868 -5.606383
7493 UBE2Z 17_28 0.6075714 43.82484 0.0004233721 -7.392405
7655 PTH1R 3_33 0.8779571 28.46963 0.0003974292 -5.646341
8882 POLR2J3 7_63 0.9604481 25.73621 0.0003930277 4.987179
1508 CWF19L1 10_64 0.6961732 33.33104 0.0003689527 -5.810127
7980 LMOD1 1_102 0.9455781 24.42585 0.0003672414 -4.906667
3290 GRB14 2_100 0.8747366 25.00435 0.0003477743 5.163265
249 ANGEL1 14_36 0.9355098 21.80009 0.0003242733 4.558286
9990 SEC24C 10_49 0.7329619 26.90018 0.0003135026 -4.862500
9611 PEAK1 15_36 0.4784997 39.01754 0.0002968563 -6.885057
5258 C2orf49 2_62 0.6887055 26.87816 0.0002943322 5.234783
1848 CTSZ 20_34 0.8804599 20.17505 0.0002824416 -3.895833
14287 RP5-899E9.1 7_49 0.8131882 19.91257 0.0002574678 -4.333333
4668 ZNF236 18_45 0.7874377 20.13940 0.0002521548 -4.378049
7322 NTAN1 16_15 0.7753888 19.37072 0.0002388196 4.191781
4021 KBTBD4 11_29 0.6072885 24.29633 0.0002346066 -5.097561
9579 DMRT2 9_1 0.7497494 19.40307 0.0002313082 -4.317647
6029 SCYL1 11_36 0.6145439 22.22566 0.0002171762 -4.813953
num_eqtl
7057 1
10241 1
3617 1
7493 1
7655 1
8882 1
1508 1
7980 1
3290 1
249 2
9990 1
9611 1
5258 1
1848 1
14287 1
4668 1
7322 1
4021 1
9579 1
6029 1Genes with largest z scores
genename region_tag susie_pip mu2 PVE z
7057 JAZF1 7_23 0.277121240 130.41581 5.746517e-04 -12.662338
2722 WFS1 4_7 0.158489875 64.77219 1.632280e-04 11.434211
3379 THADA 2_27 0.063977825 59.34224 6.036678e-05 8.666667
14565 LINC01126 2_27 0.050344112 52.17727 4.176713e-05 -8.376923
6467 CDKAL1 6_15 0.004169188 37.80537 2.506165e-06 -8.191860
7493 UBE2Z 17_28 0.607571388 43.82484 4.233721e-04 -7.392405
10525 UBE2E2 3_17 0.084142485 48.51436 6.490681e-05 7.166009
11136 KCNJ11 11_12 0.028462071 45.08258 2.040234e-05 7.075347
9611 PEAK1 15_36 0.478499702 39.01754 2.968563e-04 -6.885057
11227 NCR3LG1 11_12 0.035886976 44.07749 2.515118e-05 -6.854088
1401 PABPC4 1_24 0.103951722 42.78419 7.071631e-05 -6.817204
3273 NRBP1 2_16 0.057481036 43.85515 4.008204e-05 -6.625000
12062 MICB 6_25 0.392658326 34.75289 2.169753e-04 6.462427
12780 CYP21A2 6_26 0.055454852 39.91456 3.519456e-05 6.452632
10241 ZNF664 12_75 0.739843464 41.10919 4.835967e-04 -6.452055
7491 ATP5G1 17_28 0.090094897 41.34788 5.923222e-05 6.400000
7378 AP3S2 15_41 0.369115688 36.18157 2.123511e-04 6.356322
7494 SNF8 17_28 0.077698290 39.44087 4.872620e-05 6.300000
13095 ARPIN 15_41 0.224871053 34.65071 1.238940e-04 6.250000
3656 CCDC92 12_75 0.135611254 42.88152 9.246353e-05 -5.886761
num_eqtl
7057 1
2722 1
3379 1
14565 1
6467 1
7493 1
10525 2
11136 2
9611 1
11227 2
1401 1
3273 1
12062 2
12780 1
10241 1
7491 1
7378 1
7494 1
13095 1
3656 2Comparing z scores and PIPs
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
[1] 0.008092765 genename region_tag susie_pip mu2 PVE z
7057 JAZF1 7_23 0.277121240 130.41581 5.746517e-04 -12.662338
2722 WFS1 4_7 0.158489875 64.77219 1.632280e-04 11.434211
3379 THADA 2_27 0.063977825 59.34224 6.036678e-05 8.666667
14565 LINC01126 2_27 0.050344112 52.17727 4.176713e-05 -8.376923
6467 CDKAL1 6_15 0.004169188 37.80537 2.506165e-06 -8.191860
7493 UBE2Z 17_28 0.607571388 43.82484 4.233721e-04 -7.392405
10525 UBE2E2 3_17 0.084142485 48.51436 6.490681e-05 7.166009
11136 KCNJ11 11_12 0.028462071 45.08258 2.040234e-05 7.075347
9611 PEAK1 15_36 0.478499702 39.01754 2.968563e-04 -6.885057
11227 NCR3LG1 11_12 0.035886976 44.07749 2.515118e-05 -6.854088
1401 PABPC4 1_24 0.103951722 42.78419 7.071631e-05 -6.817204
3273 NRBP1 2_16 0.057481036 43.85515 4.008204e-05 -6.625000
12062 MICB 6_25 0.392658326 34.75289 2.169753e-04 6.462427
12780 CYP21A2 6_26 0.055454852 39.91456 3.519456e-05 6.452632
10241 ZNF664 12_75 0.739843464 41.10919 4.835967e-04 -6.452055
7491 ATP5G1 17_28 0.090094897 41.34788 5.923222e-05 6.400000
7378 AP3S2 15_41 0.369115688 36.18157 2.123511e-04 6.356322
7494 SNF8 17_28 0.077698290 39.44087 4.872620e-05 6.300000
13095 ARPIN 15_41 0.224871053 34.65071 1.238940e-04 6.250000
3656 CCDC92 12_75 0.135611254 42.88152 9.246353e-05 -5.886761
num_eqtl
7057 1
2722 1
3379 1
14565 1
6467 1
7493 1
10525 2
11136 2
9611 1
11227 2
1401 1
3273 1
12062 2
12780 1
10241 1
7491 1
7378 1
7494 1
13095 1
3656 2Sensitivity, specificity and precision for silver standard genes
[1] 72[1] 23[1] 4.525006[1] 8[1] 67 genename region_tag susie_pip mu2 PVE z num_eqtl
14287 RP5-899E9.1 7_49 0.8131882 19.91257 0.0002574678 -4.333333 1
1848 CTSZ 20_34 0.8804599 20.17505 0.0002824416 -3.895833 1 ctwas TWAS
0.00000000 0.04166667 ctwas TWAS
0.9990310 0.9922481 ctwas TWAS
0.00000000 0.04477612 
| 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