Chapter 4 Practicing with Clinical Data

4.1 About the dataset

We will use the data from this paper: https://www.cell.com/cell-genomics/pdf/S2666-979X(23)00115-5.pdf

4.2 How to get the data

You can find the data here: https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master?tab=readme-ov-file#how-to-obtain-openpbta-data

4.3 Basic analyses

Walk through some basic analyses, referencing techniques from https://hutchdatascience.org/Cancer_Clinical_Informatics/

4.4 Basic plots

sessionInfo()

## R version 4.3.2 (2023-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
## 
## 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: Etc/UTC
## tzcode source: system (glibc)
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## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.34    R6_2.5.1         bookdown_0.39.1  fastmap_1.1.1   
##  [5] xfun_0.44.4      cachem_1.0.8     knitr_1.47.3     htmltools_0.5.7 
##  [9] rmarkdown_2.27.1 lifecycle_1.0.4  cli_3.6.2        sass_0.4.8      
## [13] jquerylib_0.1.4  compiler_4.3.2   tools_4.3.2      evaluate_0.23   
## [17] bslib_0.6.1      yaml_2.3.8       rlang_1.1.4      jsonlite_1.8.8