Four expression traits simulation
shengqian
2024-5-6
Last updated: 2024-06-03
Checks: 6 1
Knit directory: multigroup_ctwas_analysis/
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This four expression traits simulation study is conducted to evaluate our new cTWAS software performance (parameter estimation, PIP calibration …). Four expression traits from PredictDB are used in this study, which are Liver, Adipose, Lung and stomach. Liver and Adipose are selected as causal tissues, each with 3% PVE and 0.9% prior. Lung and stomach are non-causal tissues with 0% PVE. Two types of LD between weight SNPs (calculating gene z score) are used and compared in this study. And their performance are very close because most genes only have one weight SNP.
Simulation 1: Expression trait in liver with 3% PVE and 0.9% Prior
Number of causal genes detected (GTEX LD)
simutag ctwas_genes ctwas_cgenes twas_genes twas_cgenes total_cgenes
1 1-1 14 12 189 33 140
2 1-2 32 27 331 56 180
3 1-3 34 27 260 37 156
4 1-4 8 6 207 27 126
5 1-5 35 27 350 40 154
ctwas_genes_combined ctwas_cgenes_combined total_cgenes_combined
1 25 24 139
2 43 36 178
3 44 35 156
4 14 11 126
5 45 37 154Number of causal genes detected (UKBB LD)
simutag ctwas_genes ctwas_cgenes twas_genes twas_cgenes total_cgenes
1 1-1 13 12 189 33 140
2 1-2 26 23 327 57 180
3 1-3 25 24 255 37 156
4 1-4 6 6 207 26 126
5 1-5 33 26 351 40 154
ctwas_genes_combined ctwas_cgenes_combined total_cgenes_combined
1 24 24 139
2 41 36 178
3 34 31 156
4 14 11 126
5 42 35 154Estimated Prior Inclusion Probability and PVE (GTEX LD)
Estimated Prior Inclusion Probability and PVE (UKBB LD)
PIP attribution among tissues (UKBBLD)
PIP Calibration Plot of expression traits - Estimated Parameter (filter out cs index 0)
PIP Calibration Plot of expression traits - True Parameter (filter out cs index 0)
PIP Calibration Plot of gene level PIP - Estimated Parameter (filter out cs index 0)
PIP Calibration Plot of gene level PIP - True Parameter (filter out cs index 0)
| Version | Author | Date |
|---|---|---|
| a0efc0d | 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):
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[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
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[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
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[69] LDlinkR_1.4.0 yaml_2.3.5
[71] curl_4.3.2 gridExtra_2.3
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[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
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