Last updated: 2026-01-13

Checks: 4 2

Knit directory: ~/Documents/BP1_BloodCancer/

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Background and goals

Reviewer request: correlate BRCA1P1 copy number with TP53 mutation status in blood cancer datasets.

Datasets (TCGA PanCancer Atlas via cBioPortal downloads):

Diffuse Large B-Cell Lymphoma (TCGA-DLBC)

Acute Myeloid Leukemia (TCGA-LAML)

High-level workflow (per dataset):

Define TP53 status per sample from the mutation download (Mut vs WT).

Use CNV segmentation to extract the CNV segment that overlaps the BRCA1P1 locus.

Select one CNV segment per sample (max overlap; ties → shorter segment).

Compare seg.mean between TP53 groups using Wilcoxon rank-sum.

Generate a plot and export a fully organized Excel workbook

4.1 TCGA-DLBC

# A tibble: 2 × 5
  TP53_group      n mean_segmean median_segmean sd_segmean
  <fct>       <int>        <dbl>          <dbl>      <dbl>
1 TP53 WT        32      0.00816        -0.0126     0.110 
2 TP53 Mutant     5      0.0123          0.0586     0.0896

    Wilcoxon rank sum exact test

data:  seg.mean by TP53_group
W = 66, p-value = 0.5598
alternative hypothesis: true location shift is not equal to 0

4.2 TCGA-LAML

# A tibble: 2 × 5
  TP53_group      n mean_segmean median_segmean sd_segmean
  <fct>       <int>        <dbl>          <dbl>      <dbl>
1 TP53 WT       174      0.00684        -0.0022     0.0713
2 TP53 Mutant    16     -0.119          -0.0439     0.178 

    Wilcoxon rank sum test with continuity correction

data:  seg.mean by TP53_group
W = 2033, p-value = 0.002344
alternative hypothesis: true location shift is not equal to 0


sessionInfo()
R version 4.5.1 (2025-06-13 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/Chicago
tzcode source: internal

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

other attached packages:
[1] openxlsx_4.2.8 ggplot2_4.0.0  tibble_3.3.0   stringr_1.5.2  dplyr_1.1.4   
[6] readxl_1.4.5  

loaded via a namespace (and not attached):
 [1] gtable_0.3.6       jsonlite_2.0.0     compiler_4.5.1     promises_1.5.0    
 [5] zip_2.3.3          tidyselect_1.2.1   Rcpp_1.1.0         git2r_0.36.2      
 [9] later_1.4.4        jquerylib_0.1.4    scales_1.4.0       yaml_2.3.10       
[13] fastmap_1.2.0      R6_2.6.1           labeling_0.4.3     generics_0.1.4    
[17] workflowr_1.7.2    knitr_1.50         rprojroot_2.1.1    RColorBrewer_1.1-3
[21] bslib_0.9.0        pillar_1.11.1      rlang_1.1.6        utf8_1.2.6        
[25] cachem_1.1.0       stringi_1.8.7      httpuv_1.6.16      xfun_0.53         
[29] S7_0.2.0           fs_1.6.6           sass_0.4.10        otel_0.2.0        
[33] cli_3.6.5          withr_3.0.2        magrittr_2.0.3     grid_4.5.1        
[37] digest_0.6.37      rstudioapi_0.17.1  lifecycle_1.0.4    vctrs_0.6.5       
[41] evaluate_1.0.5     glue_1.8.0         farver_2.1.2       cellranger_1.1.0  
[45] rmarkdown_2.30     tools_4.5.1        pkgconfig_2.0.3    htmltools_0.5.8.1