Rerunning the simulation study

Last updated: 2025-04-08

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Knit directory: DTU-code/analysis/

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Unstaged changes:
    Modified:   misc/mouse.Rmd/Figure-CaseStudy.pdf

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/simulation-howto.Rmd) and HTML (docs/simulation-howto.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	40fd9aa	Pedro Baldoni	2025-04-08	Adding new Rmd how-to

The R code used in our simulation study to generate the simulated data, quantify the FASTQ files, run DTU methods, and summarize the results was organized as an R package and it is located in the GitHub repository of this page in the directory ./code/pkg.

In our paper we have run one simulation study and analyzed it in two ways: one with a more restrictive filtering criteria (default filterByExpr function) and another with a more lenient filtering criteria, as described in our paper. In our repository, scripts to reproduce these two simulation studies are located in the directories ./code/simulation and ./code/simulation-lenient, respectively. Instructions on how to run these simulation studies are identical. Below I describe how to run the “strict” simulation. Analogous steps can be followed to reproduce the lenient simulation.

To run our simulations, readers should refer to the files stored in the directory ./code/simulation. The text file ./code/simulation/readme.txt presents the necessary steps to run the simulations and summarize the results. Briefly, readers should run the following steps:

Run the file parameters.R with, for example, the command Rscript parameters.R.
Run the SLURM script run.sh with, for example, sbatch run.sh on your HPC running the SLURM workload manager. If your HPC uses a different workload manager, please change run.sh accordingly.
Once all simulations have been completed, run the script summarize.R with, for example, the command Rscript summarize.R to summarize all the results.

Once steps 1-3 above have been completed, the Rmarkdown simulation-*.Rmd files under ./analysis can be run.

sessionInfo()

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Red Hat Enterprise Linux 9.3 (Plow)

Matrix products: default
BLAS:   /stornext/System/data/software/rhel/9/base/tools/R/4.4.1/lib64/R/lib/libRblas.so 
LAPACK: /stornext/System/data/software/rhel/9/base/tools/R/4.4.1/lib64/R/lib/libRlapack.so;  LAPACK version 3.12.0

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       

time zone: Australia/Melbourne
tzcode source: system (glibc)

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

other attached packages:
[1] workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] jsonlite_1.9.1      compiler_4.4.1      BiocManager_1.30.25
 [4] renv_1.1.2          promises_1.3.2      Rcpp_1.0.14        
 [7] stringr_1.5.1       git2r_0.35.0        callr_3.7.6        
[10] later_1.4.1         jquerylib_0.1.4     yaml_2.3.10        
[13] fastmap_1.2.0       R6_2.6.1            knitr_1.49         
[16] tibble_3.2.1        rprojroot_2.0.4     bslib_0.9.0        
[19] pillar_1.10.1       rlang_1.1.5         cachem_1.1.0       
[22] stringi_1.8.4       httpuv_1.6.15       xfun_0.51          
[25] getPass_0.2-4       fs_1.6.5            sass_0.4.9         
[28] cli_3.6.4           magrittr_2.0.3      ps_1.9.0           
[31] digest_0.6.37       processx_3.8.6      rstudioapi_0.17.1  
[34] lifecycle_1.0.4     vctrs_0.6.5         evaluate_1.0.3     
[37] glue_1.8.0          whisker_0.4.1       rmarkdown_2.29     
[40] httr_1.4.7          tools_4.4.1         pkgconfig_2.0.3    
[43] htmltools_0.5.8.1

Rerunning the simulation study

Pedro Baldoni

08 April, 2025