Last updated: 2022-07-12

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Knit directory: EMBL2016/analysis/

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Process drug screen data

Use trepazoidal AUCs as response variables.

Association with outcomes

Subset survival table

How many patients have outcome data?

[1] 130

Functions for outcome associations

P-value adjustment

Gene associated with either TTT or OS at 10% FDR

P-value histograms

TTT - Univariate test

TTT - Multi-variate test (including IGHV as co-variate)

OS

OS - Multi-variate test (including IGHV as covariate)

Table of associations

  • In the table, the columns with prefix “p” indicate p-value, “hr” indicate hazard ratio for the associations between drug responses and clinical outcomes.
  • The columns with suffix “.multi” include the p values and hazard ratio from multi-variate models with IGHV status as a covariate, to identify associations independent of IGHV status.
  • The suffix “.adj” indicates adjusted p-values.
  • Only the drugs with significant associations (adjusted p-values < 0.1) with either TTT or OS in uni-variate test are shown in this table.

KM plots

KM plots of significant association in univariate test.

KM plot in pdf format

pdf file

KM plots of significant associations in multi-variate test

pdf file
In those plots, samples are grouped based on both IGHV status and the drug response. The median response values are used to define the sensitive and resistant samples.


R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur/Monterey 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] forcats_0.5.1               stringr_1.4.0              
 [3] dplyr_1.0.9                 purrr_0.3.4                
 [5] readr_2.1.2                 tidyr_1.2.0                
 [7] tibble_3.1.7                tidyverse_1.3.1            
 [9] survminer_0.4.9             ggpubr_0.4.0               
[11] survival_3.3-1              cowplot_1.1.1              
[13] maxstat_0.7-25              ggrepel_0.9.1              
[15] ggbeeswarm_0.6.0            ggplot2_3.3.6              
[17] DESeq2_1.36.0               SummarizedExperiment_1.26.1
[19] Biobase_2.56.0              MatrixGenerics_1.8.0       
[21] matrixStats_0.62.0          GenomicRanges_1.48.0       
[23] GenomeInfoDb_1.32.2         IRanges_2.30.0             
[25] S4Vectors_0.34.0            BiocGenerics_0.42.0        

loaded via a namespace (and not attached):
  [1] colorspace_2.0-3       ggsignif_0.6.3         ellipsis_0.3.2        
  [4] rprojroot_2.0.3        XVector_0.36.0         fs_1.5.2              
  [7] rstudioapi_0.13        DT_0.23                bit64_4.0.5           
 [10] lubridate_1.8.0        AnnotationDbi_1.58.0   fansi_1.0.3           
 [13] mvtnorm_1.1-3          xml2_1.3.3             codetools_0.2-18      
 [16] splines_4.2.0          cachem_1.0.6           geneplotter_1.74.0    
 [19] knitr_1.39             jsonlite_1.8.0         workflowr_1.7.0       
 [22] broom_0.8.0            km.ci_0.5-6            annotate_1.74.0       
 [25] dbplyr_2.2.0           png_0.1-7              compiler_4.2.0        
 [28] httr_1.4.3             backports_1.4.1        assertthat_0.2.1      
 [31] Matrix_1.4-1           fastmap_1.1.0          cli_3.3.0             
 [34] later_1.3.0            htmltools_0.5.2        tools_4.2.0           
 [37] gtable_0.3.0           glue_1.6.2             GenomeInfoDbData_1.2.8
 [40] Rcpp_1.0.8.3           carData_3.0-5          cellranger_1.1.0      
 [43] jquerylib_0.1.4        vctrs_0.4.1            Biostrings_2.64.0     
 [46] crosstalk_1.2.0        exactRankTests_0.8-35  xfun_0.31             
 [49] rvest_1.0.2            lifecycle_1.0.1        rstatix_0.7.0         
 [52] XML_3.99-0.10          zoo_1.8-10             zlibbioc_1.42.0       
 [55] scales_1.2.0           hms_1.1.1              promises_1.2.0.1      
 [58] parallel_4.2.0         RColorBrewer_1.1-3     yaml_2.3.5            
 [61] memoise_2.0.1          gridExtra_2.3          KMsurv_0.1-5          
 [64] sass_0.4.1             stringi_1.7.6          RSQLite_2.2.14        
 [67] highr_0.9              genefilter_1.78.0      BiocParallel_1.30.3   
 [70] rlang_1.0.2            pkgconfig_2.0.3        bitops_1.0-7          
 [73] evaluate_0.15          lattice_0.20-45        htmlwidgets_1.5.4     
 [76] bit_4.0.4              tidyselect_1.1.2       magrittr_2.0.3        
 [79] R6_2.5.1               generics_0.1.2         DelayedArray_0.22.0   
 [82] DBI_1.1.3              haven_2.5.0            pillar_1.7.0          
 [85] withr_2.5.0            KEGGREST_1.36.2        abind_1.4-5           
 [88] RCurl_1.98-1.7         modelr_0.1.8           crayon_1.5.1          
 [91] car_3.1-0              survMisc_0.5.6         utf8_1.2.2            
 [94] tzdb_0.3.0             rmarkdown_2.14         readxl_1.4.0          
 [97] locfit_1.5-9.5         grid_4.2.0             data.table_1.14.2     
[100] blob_1.2.3             git2r_0.30.1           reprex_2.0.1          
[103] digest_0.6.29          xtable_1.8-4           httpuv_1.6.5          
[106] munsell_0.5.0          beeswarm_0.4.0         vipor_0.4.5           
[109] bslib_0.3.1