Simulation for donor effect

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Last updated: 2024-11-09

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Knit directory: DEanalysis/

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Visulization of Donor effect and DE effect

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Simulation results

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# A tibble: 36 × 3
   Configuration  Method               Average_Runtime
   <chr>          <fct>                          <dbl>
 1 Donor0.5_DE0.5 Poisson-glmm_UMI_new           57.2 
 2 Donor0.5_DE1   Poisson-glmm_UMI_new           55.4 
 3 Donor1_DE0.5   Poisson-glmm_UMI_new           64.3 
 4 Donor1_DE1     Poisson-glmm_UMI_new           64.4 
 5 Donor0.5_DE0.5 Poisson-glmm_UMI_old           57.2 
 6 Donor0.5_DE1   Poisson-glmm_UMI_old           55.4 
 7 Donor1_DE0.5   Poisson-glmm_UMI_old           64.3 
 8 Donor1_DE1     Poisson-glmm_UMI_old           64.4 
 9 Donor0.5_DE0.5 Binomial-glmm_UMI              39.0 
10 Donor0.5_DE1   Binomial-glmm_UMI              37.5 
11 Donor1_DE0.5   Binomial-glmm_UMI              42.1 
12 Donor1_DE1     Binomial-glmm_UMI              42.2 
13 Donor0.5_DE0.5 MAST_CPM                       21.3 
14 Donor0.5_DE1   MAST_CPM                       18.8 
15 Donor1_DE0.5   MAST_CPM                       17.5 
16 Donor1_DE1     MAST_CPM                       17.3 
17 Donor0.5_DE0.5 Wilcox_Norm                     2.37
18 Donor0.5_DE1   Wilcox_Norm                     3.04
19 Donor1_DE0.5   Wilcox_Norm                     2.37
20 Donor1_DE1     Wilcox_Norm                     2.98
21 Donor0.5_DE0.5 pb-DESeq2_UMI                   3.29
22 Donor0.5_DE1   pb-DESeq2_UMI                   3.21
23 Donor1_DE0.5   pb-DESeq2_UMI                   3.21
24 Donor1_DE1     pb-DESeq2_UMI                   3.22
25 Donor0.5_DE0.5 pb-edgeR_cpm                    2.07
26 Donor0.5_DE1   pb-edgeR_cpm                    2.07
27 Donor1_DE0.5   pb-edgeR_cpm                    2.05
28 Donor1_DE1     pb-edgeR_cpm                    2.06
29 Donor0.5_DE0.5 MMvst_VST                      56.9 
30 Donor0.5_DE1   MMvst_VST                      53.3 
31 Donor1_DE0.5   MMvst_VST                      52.3 
32 Donor1_DE1     MMvst_VST                      51.8 
33 Donor0.5_DE0.5 MMpoisson_UMI                 159.  
34 Donor0.5_DE1   MMpoisson_UMI                 151.  
35 Donor1_DE0.5   MMpoisson_UMI                 149.  
36 Donor1_DE1     MMpoisson_UMI                 149.  

Session information

R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS Monterey 12.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] tidyr_1.3.1                 gridExtra_2.3              
 [3] scater_1.32.1               ggplot2_3.5.1              
 [5] scuttle_1.14.0              splatter_1.28.0            
 [7] muscat_1.18.0               dplyr_1.1.4                
 [9] MAST_1.30.0                 SingleCellExperiment_1.26.0
[11] SummarizedExperiment_1.34.0 Biobase_2.64.0             
[13] GenomicRanges_1.56.2        GenomeInfoDb_1.40.1        
[15] IRanges_2.38.1              S4Vectors_0.42.1           
[17] BiocGenerics_0.50.0         MatrixGenerics_1.16.0      
[19] matrixStats_1.4.1           pryr_0.1.6                 
[21] Seurat_5.1.0                SeuratObject_5.0.2         
[23] sp_2.1-4                   

loaded via a namespace (and not attached):
  [1] bitops_1.0-9              fs_1.6.4                 
  [3] spatstat.sparse_3.1-0     httr_1.4.7               
  [5] RColorBrewer_1.1-3        doParallel_1.0.17        
  [7] numDeriv_2016.8-1.1       backports_1.5.0          
  [9] tools_4.4.1               sctransform_0.4.1        
 [11] utf8_1.2.4                R6_2.5.1                 
 [13] lazyeval_0.2.2            uwot_0.2.2               
 [15] mgcv_1.9-1                GetoptLong_1.0.5         
 [17] withr_3.0.1               prettyunits_1.2.0        
 [19] progressr_0.14.0          cli_3.6.3                
 [21] spatstat.explore_3.3-2    fastDummies_1.7.4        
 [23] labeling_0.4.3            sass_0.4.9               
 [25] mvtnorm_1.3-1             spatstat.data_3.1-2      
 [27] blme_1.0-6                ggridges_0.5.6           
 [29] pbapply_1.7-2             parallelly_1.38.0        
 [31] limma_3.60.6              rstudioapi_0.17.0        
 [33] generics_0.1.3            shape_1.4.6.1            
 [35] gtools_3.9.5              ica_1.0-3                
 [37] spatstat.random_3.3-2     Matrix_1.7-1             
 [39] ggbeeswarm_0.7.2          fansi_1.0.6              
 [41] abind_1.4-8               lifecycle_1.0.4          
 [43] whisker_0.4.1             yaml_2.3.10              
 [45] edgeR_4.2.2               gplots_3.2.0             
 [47] SparseArray_1.4.8         Rtsne_0.17               
 [49] grid_4.4.1                promises_1.3.0           
 [51] crayon_1.5.3              miniUI_0.1.1.1           
 [53] lattice_0.22-6            beachmat_2.20.0          
 [55] cowplot_1.1.3             pillar_1.9.0             
 [57] knitr_1.48                ComplexHeatmap_2.20.0    
 [59] rjson_0.2.23              boot_1.3-31              
 [61] corpcor_1.6.10            future.apply_1.11.2      
 [63] codetools_0.2-20          leiden_0.4.3.1           
 [65] glue_1.8.0                spatstat.univar_3.0-1    
 [67] data.table_1.16.2         vctrs_0.6.5              
 [69] png_0.1-8                 spam_2.11-0              
 [71] Rdpack_2.6.1              gtable_0.3.5             
 [73] cachem_1.1.0              xfun_0.48                
 [75] rbibutils_2.3             S4Arrays_1.4.1           
 [77] mime_0.12                 reformulas_0.3.0         
 [79] survival_3.7-0            iterators_1.0.14         
 [81] statmod_1.5.0             fitdistrplus_1.2-1       
 [83] ROCR_1.0-11               nlme_3.1-166             
 [85] pbkrtest_0.5.3            EnvStats_3.0.0           
 [87] progress_1.2.3            RcppAnnoy_0.0.22         
 [89] rprojroot_2.0.4           bslib_0.8.0              
 [91] TMB_1.9.15                irlba_2.3.5.1            
 [93] vipor_0.4.7               KernSmooth_2.23-24       
 [95] colorspace_2.1-1          DESeq2_1.44.0            
 [97] tidyselect_1.2.1          compiler_4.4.1           
 [99] git2r_0.35.0              BiocNeighbors_1.22.0     
[101] DelayedArray_0.30.1       plotly_4.10.4            
[103] checkmate_2.3.2           caTools_1.18.3           
[105] scales_1.3.0              remaCor_0.0.18           
[107] lmtest_0.9-40             stringr_1.5.1            
[109] digest_0.6.37             goftest_1.2-3            
[111] spatstat.utils_3.1-0      minqa_1.2.8              
[113] variancePartition_1.34.0  rmarkdown_2.28           
[115] aod_1.3.3                 XVector_0.44.0           
[117] RhpcBLASctl_0.23-42       htmltools_0.5.8.1        
[119] pkgconfig_2.0.3           lme4_1.1-35.5            
[121] sparseMatrixStats_1.16.0  highr_0.11               
[123] fastmap_1.2.0             rlang_1.1.4              
[125] GlobalOptions_0.1.2       htmlwidgets_1.6.4        
[127] UCSC.utils_1.0.0          shiny_1.9.1              
[129] DelayedMatrixStats_1.26.0 farver_2.1.2             
[131] jquerylib_0.1.4           zoo_1.8-12               
[133] jsonlite_1.8.9            BiocParallel_1.38.0      
[135] BiocSingular_1.20.0       magrittr_2.0.3           
[137] GenomeInfoDbData_1.2.12   dotCall64_1.2            
[139] patchwork_1.3.0           munsell_0.5.1            
[141] Rcpp_1.0.13               viridis_0.6.5            
[143] reticulate_1.39.0         stringi_1.8.4            
[145] zlibbioc_1.50.0           MASS_7.3-61              
[147] plyr_1.8.9                parallel_4.4.1           
[149] listenv_0.9.1             ggrepel_0.9.6            
[151] deldir_2.0-4              splines_4.4.1            
[153] tensor_1.5                hms_1.1.3                
[155] circlize_0.4.16           locfit_1.5-9.10          
[157] igraph_2.1.1              spatstat.geom_3.3-3      
[159] RcppHNSW_0.6.0            reshape2_1.4.4           
[161] ScaledMatrix_1.12.0       evaluate_1.0.1           
[163] nloptr_2.1.1              foreach_1.5.2            
[165] httpuv_1.6.15             RANN_2.6.2               
[167] purrr_1.0.2               polyclip_1.10-7          
[169] future_1.34.0             clue_0.3-65              
[171] scattermore_1.2           rsvd_1.0.5               
[173] broom_1.0.7               xtable_1.8-4             
[175] fANCOVA_0.6-1             RSpectra_0.16-2          
[177] later_1.3.2               viridisLite_0.4.2        
[179] tibble_3.2.1              lmerTest_3.1-3           
[181] glmmTMB_1.1.10            beeswarm_0.4.0           
[183] cluster_2.1.6             workflowr_1.7.1          
[185] globals_0.16.3