Last updated: 2022-07-07

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Knit directory: BH3profiling/analysis/

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Unstaged changes:
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Load and preprocess BH3 profiling data

Use baseline level from DBP profiling

Prepare sample background annotations

Drug resposne data (IC50 screen)

Correlations between BH3 profile (AUC) and drug responses (AUC)

Correlation test

[1] 52

P-Value summary plot

Multi-variate model to test wehther BH3 profiling adds additional information

Prepare genomics

Genes that will be included in the multivariate model

[1] "IGHV.status" "del11q"      "del13q"      "del17p"      "trisomy12"  
[6] "NOTCH1"      "SF3B1"       "TP53"

Test

Number of associated drugs per peptide

Summarising associations using network plot

Plot interesing pairs

Scatter plot of correlations

Bar plot of explained variance

Multi-variate feature selection with LASSO penalty

Data pre-processing

BH3 profiling

Drug responses

For genomic data

Training models

Clean and integrate multi-omics data

Perform lasso regression

Ploting results

Function for plotting variance explained for each measurement

Ploting selected features

Plot all heatmaps

Correlation between BH3 profile (individual concentrations) and drug responses (AUC)

Correlation test

[1] 52

Summary heatmap plot for all concentrations

Correlation between BH3 profile (AUC) and drug (individual concentrations)

[1] 52

Summary heatmap plot for drug concentrations

Correlation with estimated in vivo responses

Table of significant associations (P<0.05)

Scatter plots showing significant associations (p <0.05)

If multiple concentrations are identified as significant, only show the most significant concentration. 


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] gtable_0.3.0                latex2exp_0.9.4            
 [3] forcats_0.5.1               stringr_1.4.0              
 [5] dplyr_1.0.9                 purrr_0.3.4                
 [7] readr_2.1.2                 tidyr_1.2.0                
 [9] tibble_3.1.7                tidyverse_1.3.1            
[11] SummarizedExperiment_1.26.1 Biobase_2.56.0             
[13] GenomicRanges_1.48.0        GenomeInfoDb_1.32.2        
[15] IRanges_2.30.0              S4Vectors_0.34.0           
[17] BiocGenerics_0.42.0         MatrixGenerics_1.8.0       
[19] matrixStats_0.62.0          igraph_1.3.2               
[21] ggraph_2.0.5                ggplot2_3.3.6              
[23] tidygraph_1.2.1             limma_3.52.2               
[25] cowplot_1.1.1               qgraph_1.9.2               
[27] jyluMisc_0.1.5             

loaded via a namespace (and not attached):
  [1] utf8_1.2.2             shinydashboard_0.7.2   tidyselect_1.1.2      
  [4] htmlwidgets_1.5.4      grid_4.2.0             BiocParallel_1.30.3   
  [7] maxstat_0.7-25         munsell_0.5.0          codetools_0.2-18      
 [10] DT_0.23                withr_2.5.0            colorspace_2.0-3      
 [13] highr_0.9              knitr_1.39             rstudioapi_0.13       
 [16] ggsignif_0.6.3         labeling_0.4.2         git2r_0.30.1          
 [19] slam_0.1-50            GenomeInfoDbData_1.2.8 mnormt_2.1.0          
 [22] KMsurv_0.1-5           polyclip_1.10-0        farver_2.1.0          
 [25] rprojroot_2.0.3        vctrs_0.4.1            generics_0.1.2        
 [28] TH.data_1.1-1          xfun_0.31              sets_1.0-21           
 [31] R6_2.5.1               graphlayouts_0.8.0     bitops_1.0-7          
 [34] fgsea_1.22.0           DelayedArray_0.22.0    assertthat_0.2.1      
 [37] promises_1.2.0.1       scales_1.2.0           multcomp_1.4-19       
 [40] nnet_7.3-17            sandwich_3.0-2         workflowr_1.7.0       
 [43] rlang_1.0.2            splines_4.2.0          rstatix_0.7.0         
 [46] broom_0.8.0            checkmate_2.1.0        yaml_2.3.5            
 [49] reshape2_1.4.4         abind_1.4-5            modelr_0.1.8          
 [52] crosstalk_1.2.0        backports_1.4.1        httpuv_1.6.5          
 [55] Hmisc_4.7-0            tools_4.2.0            relations_0.6-12      
 [58] psych_2.2.5            lavaan_0.6-11          ellipsis_0.3.2        
 [61] gplots_3.1.3           jquerylib_0.1.4        RColorBrewer_1.1-3    
 [64] Rcpp_1.0.8.3           plyr_1.8.7             base64enc_0.1-3       
 [67] visNetwork_2.1.0       zlibbioc_1.42.0        RCurl_1.98-1.7        
 [70] ggpubr_0.4.0           rpart_4.1.16           pbapply_1.5-0         
 [73] viridis_0.6.2          zoo_1.8-10             haven_2.5.0           
 [76] ggrepel_0.9.1          cluster_2.1.3          exactRankTests_0.8-35 
 [79] fs_1.5.2               magrittr_2.0.3         data.table_1.14.2     
 [82] reprex_2.0.1           survminer_0.4.9        mvtnorm_1.1-3         
 [85] hms_1.1.1              shinyjs_2.1.0          mime_0.12             
 [88] evaluate_0.15          xtable_1.8-4           jpeg_0.1-9            
 [91] readxl_1.4.0           gridExtra_2.3          compiler_4.2.0        
 [94] KernSmooth_2.23-20     crayon_1.5.1           htmltools_0.5.2       
 [97] mgcv_1.8-40            corpcor_1.6.10         later_1.3.0           
[100] tzdb_0.3.0             Formula_1.2-4          lubridate_1.8.0       
[103] DBI_1.1.3              tweenr_1.0.2           dbplyr_2.2.0          
[106] MASS_7.3-57            Matrix_1.4-1           car_3.1-0             
[109] cli_3.3.0              marray_1.74.0          parallel_4.2.0        
[112] pkgconfig_2.0.3        km.ci_0.5-6            foreign_0.8-82        
[115] piano_2.12.0           xml2_1.3.3             pbivnorm_0.6.0        
[118] bslib_0.3.1            XVector_0.36.0         drc_3.0-1             
[121] rvest_1.0.2            digest_0.6.29          cellranger_1.1.0      
[124] rmarkdown_2.14         fastmatch_1.1-3        survMisc_0.5.6        
[127] htmlTable_2.4.0        shiny_1.7.1            gtools_3.9.2.2        
[130] lifecycle_1.0.1        nlme_3.1-158           glasso_1.11           
[133] jsonlite_1.8.0         carData_3.0-5          viridisLite_0.4.0     
[136] fansi_1.0.3            pillar_1.7.0           lattice_0.20-45       
[139] fastmap_1.1.0          httr_1.4.3             plotrix_3.8-2         
[142] survival_3.3-1         glue_1.6.2             fdrtool_1.2.17        
[145] png_0.1-7              ggforce_0.3.3          stringi_1.7.6         
[148] sass_0.4.1             latticeExtra_0.6-29    caTools_1.18.2