Expression and Splicing from three tissues simulations
shengqian
2023-12-30
Last updated: 2024-01-23
Checks: 7 0
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 three settings:
- 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 E from three tissues, 0% PVE, 0% \(\pi\) for S from three tissues and 30% PVE, 2.5e-4 \(\pi\) for SNP.
- 3% PVE, 0.9% \(\pi\) for Liver E, Liver S and Lung E, 0% PVE, 0% \(\pi\) for the others and 30% PVE, 2.5e-4 \(\pi\) for SNP.
Findings: I think there are still correlations between E and S within a tissues. For example, in the first case, we see inflations in the PIP calibration plots.
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
Estimated Enrichment
Simulation 2: Expression traits from three tissues are causal (3% PVE).
Results using PIP Threshold
simutag n_causal n_detected_pip n_detected_pip_in_causal
1 2-1 222 33 27
2 2-2 259 37 32
3 2-3 241 32 30
4 2-4 246 30 26
5 2-5 248 19 16[1] 0.8675497Estimated Prior Inclusion Probability
Simulation 2: Expression traits from Liver and Lung 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 3-1 274 25 24
2 3-2 292 21 20
3 3-3 290 13 12
4 3-4 291 30 26
5 3-5 268 15 12[1] 0.9038462Estimated Prior Inclusion Probability
Estimated Enrichment
Simulation 4: Expression traits from Liver and Lung 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 4-1 779 34 28
2 4-2 731 27 22
3 4-3 764 32 24
4 4-4 740 26 22
5 4-5 853 43 36[1] 0.8148148Estimated Prior Inclusion Probability
Estimated PVE
Estimated Prior Variance
Estimated Enrichment
PIP Calibration Plot
Simulation 5: 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
Estimated Prior Variance
Estimated Enrichment
PIP Calibration Plot
PIP Calibration Plot (L1=1)
PIP Calibration Plot (True parameters)
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] plyr_1.8.8 ggpubr_0.6.0 plotrix_3.8-4 cowplot_1.1.1
[5] ggplot2_3.4.0 latex2exp_0.9.6 data.table_1.14.6 ctwas_0.1.40
[9] 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
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[25] labeling_0.4.2 stringr_1.5.0 munsell_0.5.0 broom_1.0.2
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[33] htmltools_0.5.4 tidyselect_1.2.0 tibble_3.1.8 logging_0.10-108
[37] codetools_0.2-18 fansi_1.0.3 dplyr_1.0.10 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
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[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
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