Rerunning the simulation study

Last updated: 2024-10-09

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Knit directory: GibbsDTE-code/analysis/

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Unstaged changes:
    Modified:   code/pkg/R/simulation-quant.R
    Modified:   code/pkg/R/simulation-summary.R
    Modified:   code/pkg/R/simulation-utils.R
    Modified:   code/pkg/R/simulation.R

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	529139f	Pedro Baldoni	2024-10-09	NARGAB Revision from October 2024
html	70ab63f	Pedro Baldoni	2024-04-05	Publishing workflowr
Rmd	bebf946	Pedro Baldoni	2024-04-05	Adding simulation Rmds

The R code used in our simulation study to generate the simulated data, quantify the FASTQ files, run DTE 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 two simulation studies: one designed to emulate small-scale experiments from model organisms, such as genetically identical mice or cell lines with relatively low levels of biological variation, and another designed to emulate large-scale observational experiments from human subjects with high levels of biological variation. In our repository, scripts to reproduce these two simulation studies are located in the directories ./code/simulation and ./code/simulation-large, respectively. Instructions on how to run these simulation studies are identical. Below I describe how to run the small-scale simulation. Analogous steps can be followed to reproduce the large-scale simulation. See readme.txt in ./code/simulation and ./code/simulation-large for further details.

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 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 9.4 (Plow)

Matrix products: default
BLAS:   /stornext/System/data/software/rhel/9/base/tools/R/4.3.3/lib64/R/lib/libRblas.so 
LAPACK: /stornext/System/data/software/rhel/9/base/tools/R/4.3.3/lib64/R/lib/libRlapack.so;  LAPACK version 3.11.0

locale:
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 [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_1.8.9      compiler_4.3.3      BiocManager_1.30.25
 [4] renv_1.0.9          promises_1.3.0      Rcpp_1.0.13        
 [7] stringr_1.5.1       git2r_0.33.0        callr_3.7.6        
[10] later_1.3.2         jquerylib_0.1.4     yaml_2.3.10        
[13] fastmap_1.2.0       R6_2.5.1            knitr_1.48         
[16] tibble_3.2.1        rprojroot_2.0.4     bslib_0.8.0        
[19] pillar_1.9.0        rlang_1.1.4         utf8_1.2.4         
[22] cachem_1.1.0        stringi_1.8.4       httpuv_1.6.15      
[25] xfun_0.47           getPass_0.2-4       fs_1.6.4           
[28] sass_0.4.9          cli_3.6.3           magrittr_2.0.3     
[31] ps_1.8.0            digest_0.6.37       processx_3.8.4     
[34] rstudioapi_0.16.0   lifecycle_1.0.4     vctrs_0.6.5        
[37] evaluate_1.0.0      glue_1.8.0          whisker_0.4.1      
[40] fansi_1.0.6         rmarkdown_2.28      httr_1.4.7         
[43] tools_4.3.3         pkgconfig_2.0.3     htmltools_0.5.8.1

Rerunning the simulation study

Pedro Baldoni

09 October, 2024