T2D - Liver
sheng Qian
2021-2-6
Last updated: 2022-02-13
Checks: 6 1
Knit directory: cTWAS_analysis/
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| /project2/xinhe/shengqian/cTWAS/cTWAS_analysis/code/ctwas_config.R | code/ctwas_config.R |
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | eb13ecf | sq-96 | 2022-02-13 | update |
| html | e6bc169 | sq-96 | 2022-02-13 | Build site. |
| Rmd | 87fee8b | sq-96 | 2022-02-13 | update |
Weight QC
[1] 10290
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
1015 728 627 403 457 577 509 392 388 394 607 572 190 353 340 483
17 18 19 20 21 22
629 151 808 290 108 269 [1] 8215[1] 0.7983479Load 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
0.0041007085 0.0001802713 gene snp
4.388896 1.534856 [1] 337159[1] 10290 7535010 gene snp
0.0005492813 0.0061836269 [1] 0.004834584 0.111688709Genes with highest PIPs
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
genename region_tag susie_pip mu2 PVE z
3212 CCND2 12_4 0.9959793 27.97577 8.264138e-05 5.657050
2240 SEC23IP 10_74 0.6381754 61.38049 1.161811e-04 -3.610724
12661 LINC01126 2_27 0.4142141 28.18774 3.462982e-05 4.620415
10283 MCMBP 10_74 0.3685673 60.32290 6.594232e-05 3.522402
703 GUCY2C 12_12 0.2541535 35.09246 2.645301e-05 3.878767
6307 NUS1 6_78 0.2350043 32.14897 2.240826e-05 3.716370
12541 RP6-65G23.5 14_33 0.2244479 30.24036 2.013111e-05 3.369949
5911 CIZ1 9_66 0.2067132 30.11029 1.846071e-05 -3.513905
6558 AP3S2 15_41 0.1990701 30.35974 1.792543e-05 -3.745658
7641 NDEL1 17_8 0.1907755 28.90161 1.635346e-05 -3.136833
10118 RABL6 9_74 0.1894969 30.14016 1.693998e-05 3.491221
2577 GNPTAB 12_61 0.1868989 29.62473 1.642201e-05 3.600816
4089 UBAC1 9_72 0.1742949 28.55651 1.476233e-05 3.438703
9318 LIPF 10_56 0.1709291 29.37002 1.488969e-05 -2.991710
12431 RP11-535A5.1 18_11 0.1656953 28.08816 1.380381e-05 -2.997627
12123 UPK3BL 7_63 0.1607226 28.40836 1.354217e-05 3.134982
1624 TPD52L2 20_38 0.1531083 28.20869 1.280993e-05 -3.090905
1483 RPL3 22_16 0.1466952 27.86306 1.212300e-05 3.284537
4539 ISCA1 9_44 0.1449422 27.76422 1.193563e-05 3.269765
3541 ARHGAP9 12_36 0.1430809 26.51095 1.125051e-05 2.925673
num_eqtl
3212 1
2240 1
12661 1
10283 1
703 1
6307 1
12541 1
5911 2
6558 1
7641 1
10118 1
2577 1
4089 1
9318 1
12431 1
12123 1
1624 1
1483 1
4539 1
3541 1Genes with largest effect sizes
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
genename region_tag susie_pip mu2 PVE z
2240 SEC23IP 10_74 0.6381754 61.38049 1.161811e-04 -3.610724
10283 MCMBP 10_74 0.3685673 60.32290 6.594232e-05 3.522402
703 GUCY2C 12_12 0.2541535 35.09246 2.645301e-05 3.878767
8349 GPHN 14_32 0.1374525 33.29520 1.357374e-05 -3.426575
6307 NUS1 6_78 0.2350043 32.14897 2.240826e-05 3.716370
6558 AP3S2 15_41 0.1990701 30.35974 1.792543e-05 -3.745658
12541 RP6-65G23.5 14_33 0.2244479 30.24036 2.013111e-05 3.369949
10118 RABL6 9_74 0.1894969 30.14016 1.693998e-05 3.491221
5911 CIZ1 9_66 0.2067132 30.11029 1.846071e-05 -3.513905
5073 ETNK1 12_16 0.1407134 29.98608 1.251470e-05 3.169725
7288 AGGF1 5_45 0.1050999 29.89108 9.317706e-06 -3.154473
2577 GNPTAB 12_61 0.1868989 29.62473 1.642201e-05 3.600816
9318 LIPF 10_56 0.1709291 29.37002 1.488969e-05 -2.991710
7641 NDEL1 17_8 0.1907755 28.90161 1.635346e-05 -3.136833
4089 UBAC1 9_72 0.1742949 28.55651 1.476233e-05 3.438703
12123 UPK3BL 7_63 0.1607226 28.40836 1.354217e-05 3.134982
1624 TPD52L2 20_38 0.1531083 28.20869 1.280993e-05 -3.090905
12661 LINC01126 2_27 0.4142141 28.18774 3.462982e-05 4.620415
12431 RP11-535A5.1 18_11 0.1656953 28.08816 1.380381e-05 -2.997627
1460 PPP6R2 22_24 0.1361427 27.99436 1.130395e-05 -3.283527
num_eqtl
2240 1
10283 1
703 1
8349 2
6307 1
6558 1
12541 1
10118 1
5911 2
5073 1
7288 2
2577 1
9318 1
7641 1
4089 1
12123 1
1624 1
12661 1
12431 1
1460 1Genes with highest PVE
genename region_tag susie_pip mu2 PVE z
2240 SEC23IP 10_74 0.6381754 61.38049 1.161811e-04 -3.610724
3212 CCND2 12_4 0.9959793 27.97577 8.264138e-05 5.657050
10283 MCMBP 10_74 0.3685673 60.32290 6.594232e-05 3.522402
12661 LINC01126 2_27 0.4142141 28.18774 3.462982e-05 4.620415
703 GUCY2C 12_12 0.2541535 35.09246 2.645301e-05 3.878767
6307 NUS1 6_78 0.2350043 32.14897 2.240826e-05 3.716370
12541 RP6-65G23.5 14_33 0.2244479 30.24036 2.013111e-05 3.369949
5911 CIZ1 9_66 0.2067132 30.11029 1.846071e-05 -3.513905
6558 AP3S2 15_41 0.1990701 30.35974 1.792543e-05 -3.745658
10118 RABL6 9_74 0.1894969 30.14016 1.693998e-05 3.491221
2577 GNPTAB 12_61 0.1868989 29.62473 1.642201e-05 3.600816
7641 NDEL1 17_8 0.1907755 28.90161 1.635346e-05 -3.136833
9318 LIPF 10_56 0.1709291 29.37002 1.488969e-05 -2.991710
4089 UBAC1 9_72 0.1742949 28.55651 1.476233e-05 3.438703
12431 RP11-535A5.1 18_11 0.1656953 28.08816 1.380381e-05 -2.997627
8349 GPHN 14_32 0.1374525 33.29520 1.357374e-05 -3.426575
12123 UPK3BL 7_63 0.1607226 28.40836 1.354217e-05 3.134982
1624 TPD52L2 20_38 0.1531083 28.20869 1.280993e-05 -3.090905
5073 ETNK1 12_16 0.1407134 29.98608 1.251470e-05 3.169725
1483 RPL3 22_16 0.1466952 27.86306 1.212300e-05 3.284537
num_eqtl
2240 1
3212 1
10283 1
12661 1
703 1
6307 1
12541 1
5911 2
6558 1
10118 1
2577 1
7641 1
9318 1
4089 1
12431 1
8349 2
12123 1
1624 1
5073 1
1483 1Genes with largest z scores
genename region_tag susie_pip mu2 PVE z
3212 CCND2 12_4 0.99597929 27.97577 8.264138e-05 5.657050
12661 LINC01126 2_27 0.41421408 28.18774 3.462982e-05 4.620415
703 GUCY2C 12_12 0.25415347 35.09246 2.645301e-05 3.878767
6558 AP3S2 15_41 0.19907014 30.35974 1.792543e-05 -3.745658
6307 NUS1 6_78 0.23500434 32.14897 2.240826e-05 3.716370
2240 SEC23IP 10_74 0.63817542 61.38049 1.161811e-04 -3.610724
2577 GNPTAB 12_61 0.18689890 29.62473 1.642201e-05 3.600816
10283 MCMBP 10_74 0.36856732 60.32290 6.594232e-05 3.522402
1505 RBX1 22_17 0.13906601 26.28028 1.083967e-05 -3.521311
5911 CIZ1 9_66 0.20671321 30.11029 1.846071e-05 -3.513905
10118 RABL6 9_74 0.18949686 30.14016 1.693998e-05 3.491221
4089 UBAC1 9_72 0.17429489 28.55651 1.476233e-05 3.438703
10840 PPP1CB 2_17 0.08612930 23.42382 5.983755e-06 3.433773
7172 SPDYA 2_17 0.08537626 23.34966 5.912661e-06 -3.429510
8349 GPHN 14_32 0.13745250 33.29520 1.357374e-05 -3.426575
5040 CNOT6L 4_52 0.13254813 27.11893 1.066133e-05 3.423769
12541 RP6-65G23.5 14_33 0.22444790 30.24036 2.013111e-05 3.369949
1483 RPL3 22_16 0.14669520 27.86306 1.212300e-05 3.284537
1460 PPP6R2 22_24 0.13614270 27.99436 1.130395e-05 -3.283527
2417 GLRB 4_101 0.13567594 27.33830 1.100119e-05 3.269896
num_eqtl
3212 1
12661 1
703 1
6558 1
6307 1
2240 1
2577 1
10283 1
1505 1
5911 2
10118 1
4089 1
10840 3
7172 2
8349 2
5040 1
12541 1
1483 1
1460 1
2417 1Comparing z scores and PIPs
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
[1] 0.0001943635 genename region_tag susie_pip mu2 PVE z
3212 CCND2 12_4 0.99597929 27.97577 8.264138e-05 5.657050
12661 LINC01126 2_27 0.41421408 28.18774 3.462982e-05 4.620415
703 GUCY2C 12_12 0.25415347 35.09246 2.645301e-05 3.878767
6558 AP3S2 15_41 0.19907014 30.35974 1.792543e-05 -3.745658
6307 NUS1 6_78 0.23500434 32.14897 2.240826e-05 3.716370
2240 SEC23IP 10_74 0.63817542 61.38049 1.161811e-04 -3.610724
2577 GNPTAB 12_61 0.18689890 29.62473 1.642201e-05 3.600816
10283 MCMBP 10_74 0.36856732 60.32290 6.594232e-05 3.522402
1505 RBX1 22_17 0.13906601 26.28028 1.083967e-05 -3.521311
5911 CIZ1 9_66 0.20671321 30.11029 1.846071e-05 -3.513905
10118 RABL6 9_74 0.18949686 30.14016 1.693998e-05 3.491221
4089 UBAC1 9_72 0.17429489 28.55651 1.476233e-05 3.438703
10840 PPP1CB 2_17 0.08612930 23.42382 5.983755e-06 3.433773
7172 SPDYA 2_17 0.08537626 23.34966 5.912661e-06 -3.429510
8349 GPHN 14_32 0.13745250 33.29520 1.357374e-05 -3.426575
5040 CNOT6L 4_52 0.13254813 27.11893 1.066133e-05 3.423769
12541 RP6-65G23.5 14_33 0.22444790 30.24036 2.013111e-05 3.369949
1483 RPL3 22_16 0.14669520 27.86306 1.212300e-05 3.284537
1460 PPP6R2 22_24 0.13614270 27.99436 1.130395e-05 -3.283527
2417 GLRB 4_101 0.13567594 27.33830 1.100119e-05 3.269896
num_eqtl
3212 1
12661 1
703 1
6558 1
6307 1
2240 1
2577 1
10283 1
1505 1
5911 2
10118 1
4089 1
10840 3
7172 2
8349 2
5040 1
12541 1
1483 1
1460 1
2417 1Sensitivity, specificity and precision for silver standard genes
[1] 72[1] 33[1] 4.570782[1] 1[1] 2[1] genename region_tag susie_pip mu2 PVE z num_eqtl
<0 rows> (or 0-length row.names)ctwas TWAS
0 0 ctwas TWAS
0.9999025 0.9998050 ctwas TWAS
0 0 
| 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_0.4.12 jquerylib_0.1.4
[13] later_0.8.0 pillar_1.6.4 glue_1.5.1 withr_2.4.3
[17] DBI_1.1.1 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_0.5.0 highr_0.9 Rcpp_1.0.7
[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 tools_3.6.1
[45] magrittr_2.0.1 tibble_3.1.6 RSQLite_2.2.8 crayon_1.4.2
[49] whisker_0.3-2 pkgconfig_2.0.3 ellipsis_0.3.2 data.table_1.14.2
[53] assertthat_0.2.1 rmarkdown_2.11 R6_2.5.1 git2r_0.26.1
[57] compiler_3.6.1