T2D - Pancreas
sheng Qian
2021-2-6
Last updated: 2022-02-26
Checks: 6 1
Knit directory: cTWAS_analysis/
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Weight QC
[1] 7605
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
748 581 480 310 401 436 387 270 287 327 513 475 161 273 282 292 407 119 367 228
21 22
92 169 [1] 4452[1] 0.5854043Load 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
0.0123097006 0.0003667405 gene snp
8.180928 8.889625 [1] 62892[1] 7605 5017190 gene snp
0.01217738 0.26008027 [1] 0.06992339 1.44416811Genes with highest PIPs
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
genename region_tag susie_pip mu2 PVE z num_eqtl
5708 SCRN2 17_28 0.8106840 23.09802 0.0002977357 -4.970331 2
3452 ARG1 6_87 0.7825383 28.70545 0.0003571696 -5.418037 2
8741 ONECUT1 15_22 0.7596047 27.19347 0.0003284406 5.078652 1
10062 ARL6IP4 12_75 0.7433361 36.01403 0.0004256587 5.620253 1
11158 PARVA 11_9 0.7137719 21.89032 0.0002484369 -3.861836 2
2227 DNASE2 19_10 0.7083131 19.08862 0.0002149831 -3.744186 1
4461 ZNF236 18_45 0.7058864 20.69653 0.0002322934 -4.378049 1
7604 CFAP221 2_69 0.6764235 20.29448 0.0002182736 -4.049666 2
10527 GSAP 7_49 0.6504951 24.56257 0.0002540519 -4.185185 1
183 GIPR 19_32 0.6326493 36.31838 0.0003653374 -6.632184 1
1451 CWF19L1 10_64 0.6279579 33.14247 0.0003309177 -5.802916 2
12493 LINC01184 5_78 0.5774450 20.30140 0.0001863979 3.793478 1
4519 TUBG1 17_25 0.5615797 23.49127 0.0002097599 5.267913 2
6236 CRIP3 6_33 0.5552431 21.65792 0.0001912073 4.544995 2
2221 MIER2 19_1 0.5414438 23.95810 0.0002062578 3.683544 1
6019 MRPS5 2_57 0.5399310 21.72457 0.0001865065 -3.736842 1
11243 ZNF251 8_94 0.5343093 24.42065 0.0002074696 -4.886076 1
1411 TYRO3 15_15 0.5095761 23.08603 0.0001870522 4.865854 1
3830 KBTBD4 11_29 0.4950396 25.44472 0.0002002821 -5.097561 1
12664 LINC01933 5_89 0.4650992 20.73843 0.0001533649 3.780488 1Genes with largest effect sizes
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
genename region_tag susie_pip mu2 PVE z
6795 JAZF1 7_23 0.0253350265 147.33975 5.935344e-05 -13.081610
474 BCAR1 16_40 0.0891403843 58.61868 8.308357e-05 -7.720000
10584 ARAP1 11_41 0.0192135642 57.42519 1.754345e-05 7.885714
6345 CDKN2B 9_16 0.0874432759 55.90606 7.773022e-05 -8.191781
13639 LINC01126 2_27 0.0310929522 53.93953 2.666697e-05 -8.376923
10742 NCR3LG1 11_12 0.0210811758 51.25289 1.717979e-05 -7.369863
7991 NKX6-3 8_36 0.4571378966 42.54881 3.092710e-04 -6.780976
9232 PEAK1 15_36 0.4152425579 40.39351 2.666970e-04 6.885057
7192 ATP5G1 17_28 0.0676819144 39.62674 4.264475e-05 6.400000
11440 RBM20 10_70 0.0002240545 38.42672 1.368962e-07 -3.000000
7194 SNF8 17_28 0.0573205865 37.71067 3.437000e-05 6.300000
1291 P2RX7 12_74 0.2975091723 37.48946 1.773430e-04 5.483748
10224 BMP8A 1_24 0.0347386872 37.42298 2.067076e-05 6.296296
7087 AP3S2 15_41 0.3727948286 37.36237 2.214669e-04 6.356322
183 GIPR 19_32 0.6326492659 36.31838 3.653374e-04 -6.632184
10062 ARL6IP4 12_75 0.7433361169 36.01403 4.256587e-04 5.620253
10674 HAPLN4 19_15 0.0946101030 35.80928 5.386884e-05 5.347368
11533 MICB 6_25 0.0933548640 33.28052 4.940054e-05 5.545585
1451 CWF19L1 10_64 0.6279578506 33.14247 3.309177e-04 -5.802916
8540 TAP1 6_27 0.0647763566 32.26518 3.323190e-05 -5.575000
num_eqtl
6795 2
474 1
10584 1
6345 1
13639 1
10742 1
7991 2
9232 1
7192 1
11440 1
7194 1
1291 2
10224 1
7087 1
183 1
10062 1
10674 1
11533 2
1451 2
8540 1Genes with highest PVE
genename region_tag susie_pip mu2 PVE z num_eqtl
10062 ARL6IP4 12_75 0.7433361 36.01403 0.0004256587 5.620253 1
183 GIPR 19_32 0.6326493 36.31838 0.0003653374 -6.632184 1
3452 ARG1 6_87 0.7825383 28.70545 0.0003571696 -5.418037 2
1451 CWF19L1 10_64 0.6279579 33.14247 0.0003309177 -5.802916 2
8741 ONECUT1 15_22 0.7596047 27.19347 0.0003284406 5.078652 1
7991 NKX6-3 8_36 0.4571379 42.54881 0.0003092710 -6.780976 2
5708 SCRN2 17_28 0.8106840 23.09802 0.0002977357 -4.970331 2
9232 PEAK1 15_36 0.4152426 40.39351 0.0002666970 6.885057 1
10527 GSAP 7_49 0.6504951 24.56257 0.0002540519 -4.185185 1
11158 PARVA 11_9 0.7137719 21.89032 0.0002484369 -3.861836 2
4461 ZNF236 18_45 0.7058864 20.69653 0.0002322934 -4.378049 1
7087 AP3S2 15_41 0.3727948 37.36237 0.0002214669 6.356322 1
7604 CFAP221 2_69 0.6764235 20.29448 0.0002182736 -4.049666 2
2227 DNASE2 19_10 0.7083131 19.08862 0.0002149831 -3.744186 1
4519 TUBG1 17_25 0.5615797 23.49127 0.0002097599 5.267913 2
11243 ZNF251 8_94 0.5343093 24.42065 0.0002074696 -4.886076 1
2221 MIER2 19_1 0.5414438 23.95810 0.0002062578 3.683544 1
3830 KBTBD4 11_29 0.4950396 25.44472 0.0002002821 -5.097561 1
6236 CRIP3 6_33 0.5552431 21.65792 0.0001912073 4.544995 2
1411 TYRO3 15_15 0.5095761 23.08603 0.0001870522 4.865854 1Genes with largest z scores
genename region_tag susie_pip mu2 PVE z
6795 JAZF1 7_23 0.02533503 147.33975 5.935344e-05 -13.081610
13639 LINC01126 2_27 0.03109295 53.93953 2.666697e-05 -8.376923
6345 CDKN2B 9_16 0.08744328 55.90606 7.773022e-05 -8.191781
10584 ARAP1 11_41 0.01921356 57.42519 1.754345e-05 7.885714
474 BCAR1 16_40 0.08914038 58.61868 8.308357e-05 -7.720000
10742 NCR3LG1 11_12 0.02108118 51.25289 1.717979e-05 -7.369863
9232 PEAK1 15_36 0.41524256 40.39351 2.666970e-04 6.885057
7991 NKX6-3 8_36 0.45713790 42.54881 3.092710e-04 -6.780976
183 GIPR 19_32 0.63264927 36.31838 3.653374e-04 -6.632184
7192 ATP5G1 17_28 0.06768191 39.62674 4.264475e-05 6.400000
7087 AP3S2 15_41 0.37279483 37.36237 2.214669e-04 6.356322
7194 SNF8 17_28 0.05732059 37.71067 3.437000e-05 6.300000
10224 BMP8A 1_24 0.03473869 37.42298 2.067076e-05 6.296296
1451 CWF19L1 10_64 0.62795785 33.14247 3.309177e-04 -5.802916
10062 ARL6IP4 12_75 0.74333612 36.01403 4.256587e-04 5.620253
3128 NRBP1 2_16 0.02608681 31.30510 1.298496e-05 -5.594937
8540 TAP1 6_27 0.06477636 32.26518 3.323190e-05 -5.575000
11533 MICB 6_25 0.09335486 33.28052 4.940054e-05 5.545585
3134 PPM1G 2_16 0.02636672 30.92622 1.296545e-05 -5.544304
1291 P2RX7 12_74 0.29750917 37.48946 1.773430e-04 5.483748
num_eqtl
6795 2
13639 1
6345 1
10584 1
474 1
10742 1
9232 1
7991 2
183 1
7192 1
7087 1
7194 1
10224 1
1451 2
10062 1
3128 1
8540 1
11533 2
3134 1
1291 2Comparing z scores and PIPs
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
[1] 0.006180145 genename region_tag susie_pip mu2 PVE z
6795 JAZF1 7_23 0.02533503 147.33975 5.935344e-05 -13.081610
13639 LINC01126 2_27 0.03109295 53.93953 2.666697e-05 -8.376923
6345 CDKN2B 9_16 0.08744328 55.90606 7.773022e-05 -8.191781
10584 ARAP1 11_41 0.01921356 57.42519 1.754345e-05 7.885714
474 BCAR1 16_40 0.08914038 58.61868 8.308357e-05 -7.720000
10742 NCR3LG1 11_12 0.02108118 51.25289 1.717979e-05 -7.369863
9232 PEAK1 15_36 0.41524256 40.39351 2.666970e-04 6.885057
7991 NKX6-3 8_36 0.45713790 42.54881 3.092710e-04 -6.780976
183 GIPR 19_32 0.63264927 36.31838 3.653374e-04 -6.632184
7192 ATP5G1 17_28 0.06768191 39.62674 4.264475e-05 6.400000
7087 AP3S2 15_41 0.37279483 37.36237 2.214669e-04 6.356322
7194 SNF8 17_28 0.05732059 37.71067 3.437000e-05 6.300000
10224 BMP8A 1_24 0.03473869 37.42298 2.067076e-05 6.296296
1451 CWF19L1 10_64 0.62795785 33.14247 3.309177e-04 -5.802916
10062 ARL6IP4 12_75 0.74333612 36.01403 4.256587e-04 5.620253
3128 NRBP1 2_16 0.02608681 31.30510 1.298496e-05 -5.594937
8540 TAP1 6_27 0.06477636 32.26518 3.323190e-05 -5.575000
11533 MICB 6_25 0.09335486 33.28052 4.940054e-05 5.545585
3134 PPM1G 2_16 0.02636672 30.92622 1.296545e-05 -5.544304
1291 P2RX7 12_74 0.29750917 37.48946 1.773430e-04 5.483748
num_eqtl
6795 2
13639 1
6345 1
10584 1
474 1
10742 1
9232 1
7991 2
183 1
7192 1
7087 1
7194 1
10224 1
1451 2
10062 1
3128 1
8540 1
11533 2
3134 1
1291 2Sensitivity, specificity and precision for silver standard genes
[1] 72[1] 27[1] 4.507014[1] 18[1] 47 genename region_tag susie_pip mu2 PVE z num_eqtl
6019 MRPS5 2_57 0.5399310 21.72457 0.0001865065 -3.736842 1
12493 LINC01184 5_78 0.5774450 20.30140 0.0001863979 3.793478 1
10527 GSAP 7_49 0.6504951 24.56257 0.0002540519 -4.185185 1
11158 PARVA 11_9 0.7137719 21.89032 0.0002484369 -3.861836 2
4461 ZNF236 18_45 0.7058864 20.69653 0.0002322934 -4.378049 1
2221 MIER2 19_1 0.5414438 23.95810 0.0002062578 3.683544 1
2227 DNASE2 19_10 0.7083131 19.08862 0.0002149831 -3.744186 1
7604 CFAP221 2_69 0.6764235 20.29448 0.0002182736 -4.049666 2 ctwas TWAS
0.01388889 0.01388889 ctwas TWAS
0.9977567 0.9939298 ctwas TWAS
0.05555556 0.02127660
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