Expression and Splicing from three tissues simulations
shengqian
2023-12-30
Last updated: 2024-01-27
Checks: 6 1
Knit directory: multigroup_ctwas_analysis/
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A simulation of expression and splicing traits from three tissues is conducted to evaluate cTWAS performance (parameter estimation, PIP calibration …). Three tissues used in this simulation are Liver, Lung, Spleen.
It current has two setting:
- One tissue case: 3% PVE, 0.9% \(\pi\) for E and S from Liver and 30% PVE, 2.5e-4 \(\pi\) for SNP.
- 3% PVE, 0.9% \(\pi\) for Liver E and Liver S. 0% PVE, 0% \(\pi\) for the others and 30% PVE, 2.5e-4 \(\pi\) for SNP.
Simulation 1: Expression and Splicing from Liver (3% PVE)
Results using PIP Threshold
simutag n_causal n_detected_pip n_detected_pip_in_causal
1 1-1 339 51 48
2 1-2 314 36 32
3 1-3 296 44 38
4 1-4 308 34 28
5 1-5 329 33 29[1] 0.8838384
Simulation 2: Expression and Splicing traits from Liver are causal(3% PVE).
Results using PIP Threshold
simutag n_causal n_detected_pip n_detected_pip_in_causal
1 5-1 198 24 20
2 5-2 191 14 13
3 5-3 197 17 17
4 5-4 181 26 20
5 5-5 203 11 10[1] 0.8695652Estimated Prior Inclusion Probability
Estimated PVE
PIP Calibration Plot (True parameters)
PIP Calibration Plot (True parameters, L=1)
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.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] dplyr_1.0.10 plyr_1.8.8 ggpubr_0.6.0 plotrix_3.8-4
[5] cowplot_1.1.1 ggplot2_3.4.0 latex2exp_0.9.6 data.table_1.14.6
[9] ctwas_0.1.40 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 lattice_0.20-44 tidyr_1.3.0 getPass_0.2-2
[5] ps_1.7.2 assertthat_0.2.1 rprojroot_2.0.3 digest_0.6.31
[9] foreach_1.5.2 utf8_1.2.2 R6_2.5.1 backports_1.2.1
[13] evaluate_0.19 highr_0.9 httr_1.4.4 pillar_1.8.1
[17] rlang_1.1.1 rstudioapi_0.14 car_3.1-1 whisker_0.4.1
[21] callr_3.7.3 jquerylib_0.1.4 Matrix_1.3-3 rmarkdown_2.19
[25] labeling_0.4.2 stringr_1.5.0 munsell_0.5.0 broom_1.0.2
[29] compiler_4.1.0 httpuv_1.6.7 xfun_0.35 pkgconfig_2.0.3
[33] htmltools_0.5.4 tidyselect_1.2.0 gridExtra_2.3 tibble_3.1.8
[37] logging_0.10-108 codetools_0.2-18 fansi_1.0.3 withr_2.5.0
[41] later_1.3.0 grid_4.1.0 jsonlite_1.8.4 gtable_0.3.1
[45] lifecycle_1.0.3 DBI_1.1.3 git2r_0.30.1 magrittr_2.0.3
[49] scales_1.2.1 carData_3.0-4 cli_3.6.1 stringi_1.7.8
[53] cachem_1.0.6 farver_2.1.0 ggsignif_0.6.4 fs_1.5.2
[57] promises_1.2.0.1 pgenlibr_0.3.2 bslib_0.4.1 vctrs_0.6.3
[61] generics_0.1.3 iterators_1.0.14 tools_4.1.0 glue_1.6.2
[65] purrr_1.0.2 abind_1.4-5 processx_3.8.0 fastmap_1.1.0
[69] yaml_2.3.6 colorspace_2.0-3 rstatix_0.7.2 knitr_1.41
[73] sass_0.4.4