Last updated: 2025-03-28

Checks: 7 0

Knit directory: hruban_wflow/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20250319)

The command set.seed(20250319) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: 9b107c0

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 9b107c0. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


Ignored files:
    Ignored:    .DS_Store
    Ignored:    code/rlucas/.DS_Store
    Ignored:    data/estimates/.Rapp.history

Untracked files:
    Untracked:  code/pivot_wider_pacto.R
    Untracked:  data/allfeatures_pacto.5mb.hg19.csv
    Untracked:  extdata/

Unstaged changes:
    Modified:   analysis/index.Rmd

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/fig1a.Rmd) and HTML (docs/fig1a.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 9bbcb47 Shashikant Koul 2025-03-27 Initial commit
html 9bbcb47 Shashikant Koul 2025-03-27 Initial commit

Schematic of study design showing timeline of treatment, timeline of sample collection, and molecular analyses for both the CheckPAC and the PACTO cohort. Tumor and WBCs were sequenced from patients in the CheckPAC cohort to generate a list of somatic variants present in tumor. WGMAF values were calculated in plasma samples as the number of mutant observations divided by total number of observations across all mutated positions with tumor-specific somatic mutations. ARTEMIS-DELFI scores were generated with a fixed model using fragmentation patterns, chromosomal gains and losses, and repeat elements as features. These scores were compared to progression free and overall survival data, and multivariate hazard analyses were performed.

library(here)


sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS 15.3.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/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/New_York
tzcode source: internal

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

other attached packages:
[1] here_1.0.1      workflowr_1.7.1

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