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Rmd 932e682 sq-96 2024-01-15 update

Simulation 1: Three causal tissues and four non-causal tissues

30% PVE and 2.5e-4 prior inclusion for SNPs, 3% PVE and 0.009 prior inclusion for Brain Cerebellum, Brain Hippocampus and Brain Caudate basal ganglia. 0% PVE for other tissues.

Shared effect size parameters

For the cTWAS analysis, tissues shared an effect size parameter.

results_dir <- "/project/xinhe/shengqian/cTWAS_simulation/simulation_correlated_seven_brain_tissues/"
runtag = "ukb-s80.45-3_7corr"
configtag <- 1

simutags <- paste(1, 1:5, sep = "-")
thin <- 0.1

sample_size <- 45000
PIP_threshold <- 0.8

results_df <- get_sim_joint_res(results_dir,runtag,configtag,simutags,thin,sample_size,PIP_threshold)
group_size <- results_df[[2]]
results_df <- results_df[[1]]

Results using PIP Threshold

  simutag n_causal n_detected_pip n_detected_pip_in_causal
1     1-1      211             10                        8
2     1-2      233             32                       28
3     1-3      215             21                       18
4     1-4      212             30                       29
5     1-5      254             17                       16
[1] 0.9

Results using Combined PIP Threshold

  simutag n_causal_combined n_detected_comb_pip n_detected_comb_pip_in_causal
1     1-1               209                  40                            36
2     1-2               232                  69                            55
3     1-3               212                  40                            37
4     1-4               212                  56                            52
5     1-5               253                  49                            43
[1] 0.8779528

Estimated Prior Inclusion Probability

Estimated PVE

Estimated Prior Variance

Estimated Enrichment

PIP Calibration Plot

PIP Calibration Plot (cs_index!=0)


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