T2D - Pancreas
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] 11277
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
1099 800 650 449 509 634 558 399 424 442 714 630 218 369 389 519
17 18 19 20 21 22
698 159 865 346 120 286 [1] 8525[1] 0.7559635Load 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
0.0020424708 0.0001739611 gene snp
1.630669 1.515279 [1] 337159[1] 11277 7535010 gene snp
0.0001113988 0.0058910670 [1] 0.001961437 0.108209800Genes with highest PIPs
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
genename region_tag susie_pip mu2 PVE z
6813 NUS1 6_78 0.11190974 21.57983 7.162773e-06 3.692788
13639 LINC01126 2_27 0.11047242 22.33018 7.316634e-06 4.620415
3328 HPCAL4 1_24 0.10705683 20.92925 6.645587e-06 3.385568
619 HIPK2 7_85 0.10560943 20.59309 6.450441e-06 -3.356192
9179 HPSE 4_56 0.09090366 20.16349 5.436411e-06 -3.109502
7711 PPM1K 4_59 0.09063283 19.36279 5.204977e-06 3.048188
1140 FAT1 4_120 0.08898826 19.79091 5.223526e-06 3.124110
11775 KCTD11 17_6 0.08889942 19.53064 5.149683e-06 3.073744
7483 MAGOH 1_33 0.08556249 18.78052 4.766025e-06 3.091534
12626 RP11-675F6.3 8_34 0.08551601 19.54047 4.956185e-06 3.136535
11621 NT5M 17_15 0.08489430 18.42428 4.639107e-06 3.066208
12120 KLHL7-AS1 7_20 0.08230316 19.19736 4.686226e-06 3.456104
2430 SEC23IP 10_74 0.08213382 27.68458 6.744118e-06 -3.522402
1045 MOXD1 6_87 0.07975681 18.88876 4.468240e-06 2.971004
13004 IKBKE 1_105 0.07737702 18.94081 4.346861e-06 3.066183
922 MARK3 14_54 0.07500805 18.47044 4.109134e-06 3.322034
10756 ZNF559 19_9 0.07470959 18.40947 4.079274e-06 -3.038294
2836 SERINC1 6_82 0.07341538 18.38638 4.003580e-06 -3.103585
7860 AGGF1 5_45 0.07202300 18.10416 3.867363e-06 -3.189044
7087 AP3S2 15_41 0.07086689 18.12677 3.810036e-06 -3.581700
num_eqtl
6813 2
13639 1
3328 1
619 1
9179 1
7711 1
1140 1
11775 1
7483 1
12626 2
11621 2
12120 1
2430 1
1045 3
13004 2
922 2
10756 1
2836 2
7860 2
7087 1Genes with largest effect sizes
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
genename region_tag susie_pip mu2 PVE z
2430 SEC23IP 10_74 0.08213382 27.68458 6.744118e-06 -3.522402
11263 SDAD1 4_52 0.06147185 23.27689 4.243914e-06 -3.799166
13639 LINC01126 2_27 0.11047242 22.33018 7.316634e-06 4.620415
6813 NUS1 6_78 0.11190974 21.57983 7.162773e-06 3.692788
3328 HPCAL4 1_24 0.10705683 20.92925 6.645587e-06 3.385568
619 HIPK2 7_85 0.10560943 20.59309 6.450441e-06 -3.356192
9179 HPSE 4_56 0.09090366 20.16349 5.436411e-06 -3.109502
1140 FAT1 4_120 0.08898826 19.79091 5.223526e-06 3.124110
12626 RP11-675F6.3 8_34 0.08551601 19.54047 4.956185e-06 3.136535
11775 KCTD11 17_6 0.08889942 19.53064 5.149683e-06 3.073744
7711 PPM1K 4_59 0.09063283 19.36279 5.204977e-06 3.048188
12120 KLHL7-AS1 7_20 0.08230316 19.19736 4.686226e-06 3.456104
13004 IKBKE 1_105 0.07737702 18.94081 4.346861e-06 3.066183
10530 PIP5K1C 19_4 0.06159915 18.90786 3.454478e-06 3.055707
1045 MOXD1 6_87 0.07975681 18.88876 4.468240e-06 2.971004
7483 MAGOH 1_33 0.08556249 18.78052 4.766025e-06 3.091534
922 MARK3 14_54 0.07500805 18.47044 4.109134e-06 3.322034
11621 NT5M 17_15 0.08489430 18.42428 4.639107e-06 3.066208
10756 ZNF559 19_9 0.07470959 18.40947 4.079274e-06 -3.038294
2836 SERINC1 6_82 0.07341538 18.38638 4.003580e-06 -3.103585
num_eqtl
2430 1
11263 2
13639 1
6813 2
3328 1
619 1
9179 1
1140 1
12626 2
11775 1
7711 1
12120 1
13004 2
10530 1
1045 3
7483 1
922 2
11621 2
10756 1
2836 2Genes with highest PVE
genename region_tag susie_pip mu2 PVE z
13639 LINC01126 2_27 0.11047242 22.33018 7.316634e-06 4.620415
6813 NUS1 6_78 0.11190974 21.57983 7.162773e-06 3.692788
2430 SEC23IP 10_74 0.08213382 27.68458 6.744118e-06 -3.522402
3328 HPCAL4 1_24 0.10705683 20.92925 6.645587e-06 3.385568
619 HIPK2 7_85 0.10560943 20.59309 6.450441e-06 -3.356192
9179 HPSE 4_56 0.09090366 20.16349 5.436411e-06 -3.109502
1140 FAT1 4_120 0.08898826 19.79091 5.223526e-06 3.124110
7711 PPM1K 4_59 0.09063283 19.36279 5.204977e-06 3.048188
11775 KCTD11 17_6 0.08889942 19.53064 5.149683e-06 3.073744
12626 RP11-675F6.3 8_34 0.08551601 19.54047 4.956185e-06 3.136535
7483 MAGOH 1_33 0.08556249 18.78052 4.766025e-06 3.091534
12120 KLHL7-AS1 7_20 0.08230316 19.19736 4.686226e-06 3.456104
11621 NT5M 17_15 0.08489430 18.42428 4.639107e-06 3.066208
1045 MOXD1 6_87 0.07975681 18.88876 4.468240e-06 2.971004
13004 IKBKE 1_105 0.07737702 18.94081 4.346861e-06 3.066183
11263 SDAD1 4_52 0.06147185 23.27689 4.243914e-06 -3.799166
922 MARK3 14_54 0.07500805 18.47044 4.109134e-06 3.322034
10756 ZNF559 19_9 0.07470959 18.40947 4.079274e-06 -3.038294
2836 SERINC1 6_82 0.07341538 18.38638 4.003580e-06 -3.103585
7860 AGGF1 5_45 0.07202300 18.10416 3.867363e-06 -3.189044
num_eqtl
13639 1
6813 2
2430 1
3328 1
619 1
9179 1
1140 1
7711 1
11775 1
12626 2
7483 1
12120 1
11621 2
1045 3
13004 2
11263 2
922 2
10756 1
2836 2
7860 2Genes with largest z scores
genename region_tag susie_pip mu2 PVE z
13639 LINC01126 2_27 0.11047242 22.33018 7.316634e-06 4.620415
11263 SDAD1 4_52 0.06147185 23.27689 4.243914e-06 -3.799166
6813 NUS1 6_78 0.11190974 21.57983 7.162773e-06 3.692788
7087 AP3S2 15_41 0.07086689 18.12677 3.810036e-06 -3.581700
2430 SEC23IP 10_74 0.08213382 27.68458 6.744118e-06 -3.522402
1650 RBX1 22_17 0.05667685 16.64306 2.797720e-06 -3.521311
9101 DNAJB7 22_17 0.05202223 16.09983 2.484137e-06 3.462008
12120 KLHL7-AS1 7_20 0.08230316 19.19736 4.686226e-06 3.456104
12694 RP11-108O10.2 11_66 0.04429810 15.67381 2.059326e-06 3.442454
3328 HPCAL4 1_24 0.10705683 20.92925 6.645587e-06 3.385568
619 HIPK2 7_85 0.10560943 20.59309 6.450441e-06 -3.356192
10196 SH2D7 15_36 0.05013328 16.21181 2.410586e-06 3.348970
922 MARK3 14_54 0.07500805 18.47044 4.109134e-06 3.322034
4899 ISCA1 9_44 0.06636759 18.17383 3.577403e-06 3.269765
7860 AGGF1 5_45 0.07202300 18.10416 3.867363e-06 -3.189044
10276 CRELD2 22_24 0.04657461 16.55146 2.286393e-06 3.185929
3756 KLHL7 7_20 0.04651000 15.56592 2.147268e-06 3.138791
12626 RP11-675F6.3 8_34 0.08551601 19.54047 4.956185e-06 3.136535
474 BCAR1 16_40 0.03966336 14.74818 1.734975e-06 3.130231
1617 CHKB 22_24 0.06035504 18.19411 3.256939e-06 -3.125165
num_eqtl
13639 1
11263 2
6813 2
7087 1
2430 1
1650 1
9101 1
12120 1
12694 2
3328 1
619 1
10196 1
922 2
4899 1
7860 2
10276 1
3756 3
12626 2
474 1
1617 2Comparing z scores and PIPs
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
[1] 8.867607e-05 genename region_tag susie_pip mu2 PVE z
13639 LINC01126 2_27 0.11047242 22.33018 7.316634e-06 4.620415
11263 SDAD1 4_52 0.06147185 23.27689 4.243914e-06 -3.799166
6813 NUS1 6_78 0.11190974 21.57983 7.162773e-06 3.692788
7087 AP3S2 15_41 0.07086689 18.12677 3.810036e-06 -3.581700
2430 SEC23IP 10_74 0.08213382 27.68458 6.744118e-06 -3.522402
1650 RBX1 22_17 0.05667685 16.64306 2.797720e-06 -3.521311
9101 DNAJB7 22_17 0.05202223 16.09983 2.484137e-06 3.462008
12120 KLHL7-AS1 7_20 0.08230316 19.19736 4.686226e-06 3.456104
12694 RP11-108O10.2 11_66 0.04429810 15.67381 2.059326e-06 3.442454
3328 HPCAL4 1_24 0.10705683 20.92925 6.645587e-06 3.385568
619 HIPK2 7_85 0.10560943 20.59309 6.450441e-06 -3.356192
10196 SH2D7 15_36 0.05013328 16.21181 2.410586e-06 3.348970
922 MARK3 14_54 0.07500805 18.47044 4.109134e-06 3.322034
4899 ISCA1 9_44 0.06636759 18.17383 3.577403e-06 3.269765
7860 AGGF1 5_45 0.07202300 18.10416 3.867363e-06 -3.189044
10276 CRELD2 22_24 0.04657461 16.55146 2.286393e-06 3.185929
3756 KLHL7 7_20 0.04651000 15.56592 2.147268e-06 3.138791
12626 RP11-675F6.3 8_34 0.08551601 19.54047 4.956185e-06 3.136535
474 BCAR1 16_40 0.03966336 14.74818 1.734975e-06 3.130231
1617 CHKB 22_24 0.06035504 18.19411 3.256939e-06 -3.125165
num_eqtl
13639 1
11263 2
6813 2
7087 1
2430 1
1650 1
9101 1
12120 1
12694 2
3328 1
619 1
10196 1
922 2
4899 1
7860 2
10276 1
3756 3
12626 2
474 1
1617 2Sensitivity, specificity and precision for silver standard genes
[1] 72[1] 40[1] 4.589937[1] 0[1] 1[1] genename region_tag susie_pip mu2 PVE z num_eqtl
<0 rows> (or 0-length row.names)ctwas TWAS
0 0 ctwas TWAS
1.000000 0.999911 ctwas TWAS
NaN 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