Expression and Splicing from three tissues simulations
shengqian
2023-12-30
Last updated: 2024-05-16
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, Adipose and Lung. Only expression and splicing from liver are causal, each with 3% PVE, 0.9% \(\pi\). SNPs have 30% PVE, 2.5e-4 \(\pi\).
Simulation 1: Expression and Splicing from Liver (3% PVE)
Number of causal genes detected (GTEX LD)
simutag ctwas_genes ctwas_cgenes twas_genes twas_cgenes total_cgenes
1 1-1 31 19 629 41 198
2 1-2 19 11 441 27 191
3 1-3 21 20 786 36 197
4 1-4 24 17 751 44 181
5 1-5 23 15 534 34 203
ctwas_genes_combined ctwas_cgenes_combined total_cgenes_combined
1 34 21 198
2 20 13 191
3 21 20 197
4 26 19 181
5 28 21 203Number of causal genes detected (UKBB LD)
simutag ctwas_genes ctwas_cgenes twas_genes twas_cgenes total_cgenes
1 1-1 23 20 621 41 198
2 1-2 17 15 440 28 191
3 1-3 21 20 781 35 197
4 1-4 22 16 749 44 181
5 1-5 14 12 530 34 203
ctwas_genes_combined ctwas_cgenes_combined total_cgenes_combined
1 25 21 198
2 18 16 191
3 21 20 197
4 24 18 181
5 24 21 203Estimated Prior Inclusion Probability and PVE (GTEX LD)
Estimated Prior Inclusion Probability and PVE (UKBB LD)
| Version | Author | Date |
|---|---|---|
| 6e35c53 | sq-96 | 2024-05-16 |
PIP Calibration Plot based on GTEX LD (filter out cs index 0)
| Version | Author | Date |
|---|---|---|
| 6e35c53 | sq-96 | 2024-05-16 |
PIP Calibration Plot of expression traits (filter out cs index 0)
| Version | Author | Date |
|---|---|---|
| 6e35c53 | sq-96 | 2024-05-16 |
PIP Calibration Plot of expression traits with region merge (filter out cs index 0)
| Version | Author | Date |
|---|---|---|
| 6e35c53 | sq-96 | 2024-05-16 |
PIP Calibration Plot of gene level PIP (filter out cs index 0)
| Version | Author | Date |
|---|---|---|
| 6e35c53 | sq-96 | 2024-05-16 |
PIP Calibration Plot of gene level PIP with region merge (filter out cs index 0)
| Version | Author | Date |
|---|---|---|
| 6e35c53 | sq-96 | 2024-05-16 |
sessionInfo()R version 4.2.0 (2022-04-22)
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_1.1.4 plyr_1.8.7 plotrix_3.8-2 cowplot_1.1.1
[5] ggpubr_0.6.0 ggplot2_3.4.4 data.table_1.14.2 ctwas_0.2.1.9000
[9] workflowr_1.7.0
loaded via a namespace (and not attached):
[1] colorspace_2.0-3 ggsignif_0.6.3
[3] rjson_0.2.21 ellipsis_0.3.2
[5] rprojroot_2.0.3 XVector_0.36.0
[7] locuszoomr_0.3.0 GenomicRanges_1.48.0
[9] fs_1.5.2 rstudioapi_0.14
[11] farver_2.1.1 ggrepel_0.9.4
[13] bit64_4.0.5 AnnotationDbi_1.58.0
[15] fansi_1.0.3 xml2_1.3.3
[17] codetools_0.2-18 logging_0.10-108
[19] cachem_1.0.6 knitr_1.40
[21] jsonlite_1.8.8 Rsamtools_2.12.0
[23] broom_1.0.5 dbplyr_2.5.0
[25] png_0.1-7 compiler_4.2.0
[27] httr_1.4.4 backports_1.4.1
[29] Matrix_1.5-3 fastmap_1.1.0
[31] lazyeval_0.2.2 cli_3.6.1
[33] later_1.3.0 htmltools_0.5.3
[35] prettyunits_1.1.1 tools_4.2.0
[37] gtable_0.3.1 glue_1.6.2
[39] GenomeInfoDbData_1.2.8 rappdirs_0.3.3
[41] Rcpp_1.0.9 carData_3.0-5
[43] Biobase_2.56.0 jquerylib_0.1.4
[45] vctrs_0.6.4 Biostrings_2.64.0
[47] rtracklayer_1.56.0 xfun_0.32
[49] stringr_1.5.0 ps_1.7.1
[51] irlba_2.3.5 lifecycle_1.0.4
[53] restfulr_0.0.14 ensembldb_2.20.2
[55] rstatix_0.7.2 XML_3.99-0.14
[57] getPass_0.2-2 zlibbioc_1.42.0
[59] zoo_1.8-10 scales_1.2.1
[61] gggrid_0.2-0 hms_1.1.2
[63] promises_1.2.0.1 MatrixGenerics_1.8.0
[65] ProtGenerics_1.28.0 parallel_4.2.0
[67] SummarizedExperiment_1.26.1 AnnotationFilter_1.20.0
[69] LDlinkR_1.4.0 yaml_2.3.5
[71] curl_4.3.2 gridExtra_2.3
[73] memoise_2.0.1 sass_0.4.2
[75] biomaRt_2.52.0 stringi_1.7.8
[77] RSQLite_2.2.14 highr_0.9
[79] S4Vectors_0.34.0 BiocIO_1.6.0
[81] GenomicFeatures_1.48.3 BiocGenerics_0.42.0
[83] filelock_1.0.2 BiocParallel_1.30.3
[85] GenomeInfoDb_1.32.2 rlang_1.1.1
[87] pkgconfig_2.0.3 matrixStats_0.62.0
[89] bitops_1.0-7 evaluate_0.16
[91] lattice_0.20-45 purrr_1.0.2
[93] labeling_0.4.2 GenomicAlignments_1.32.0
[95] htmlwidgets_1.5.4 bit_4.0.4
[97] processx_3.7.0 tidyselect_1.2.1
[99] magrittr_2.0.3 R6_2.5.1
[101] IRanges_2.30.0 generics_0.1.3
[103] DelayedArray_0.22.0 DBI_1.1.3
[105] withr_2.5.0 pgenlibr_0.3.2
[107] pillar_1.9.0 whisker_0.4
[109] abind_1.4-5 mixsqp_0.3-48
[111] KEGGREST_1.36.2 RCurl_1.98-1.7
[113] tibble_3.2.1 car_3.1-1
[115] crayon_1.5.1 utf8_1.2.2
[117] BiocFileCache_2.4.0 plotly_4.10.0
[119] rmarkdown_2.16 progress_1.2.2
[121] grid_4.2.0 blob_1.2.3
[123] callr_3.7.2 git2r_0.30.1
[125] digest_0.6.29 tidyr_1.3.1
[127] httpuv_1.6.5 stats4_4.2.0
[129] munsell_0.5.0 viridisLite_0.4.1
[131] bslib_0.4.0