Contents

0.1 Instalation

if (!require("BiocManager"))
  install.packages("BiocManager")
BiocManager::install("glmSparseNet")

1 Required Packages

library(futile.logger)
library(ggplot2)
library(glmSparseNet)
library(survival)

# Some general options for futile.logger the debugging package
.Last.value <- flog.layout(layout.format('[~l] ~m'))
.Last.value <- glmSparseNet:::show.message(FALSE)
# Setting ggplot2 default theme as minimal
theme_set(ggplot2::theme_minimal())

1.1 Prepare data

data('cancer', package = 'survival')
xdata <- survival::ovarian[,c('age', 'resid.ds')]
ydata <- data.frame(
  time = survival::ovarian$futime,
  status = survival::ovarian$fustat
)

1.2 Separate using age as co-variate

(group cutoff is median calculated relative risk)

res.age <- separate2GroupsCox(c(age = 1, 0), xdata, ydata)

1.2.1 Kaplan-Meier survival results

## Call: survfit(formula = survival::Surv(time, status) ~ group, data = prognostic.index.df)
## 
##            n events median 0.95LCL 0.95UCL
## Low risk  13      4     NA     638      NA
## High risk 13      8    464     268      NA

1.2.2 Plot

A individual is attributed to low-risk group if its calculated relative risk (using Cox Proportional model) is below or equal the median risk.

The opposite for the high-risk groups, populated with individuals above the median relative-risk.

1.3 Separate using age as co-variate (group cutoff is 40% - 60%)

res.age.40.60 <- 
  separate2GroupsCox(c(age = 1, 0), 
                     xdata, 
                     ydata, 
                     probs = c(.4, .6)
  )

1.3.1 Kaplan-Meier survival results

## Call: survfit(formula = survival::Surv(time, status) ~ group, data = prognostic.index.df)
## 
##            n events median 0.95LCL 0.95UCL
## Low risk  11      3     NA     563      NA
## High risk 10      7    359     156      NA

1.3.2 Plot

A individual is attributed to low-risk group if its calculated relative risk (using Cox Proportional model) is below the median risk.

The opposite for the high-risk groups, populated with individuals above the median relative-risk.

1.4 Separate using age as co-variate (group cutoff is 60% - 40%)

This is a special case where you want to use a cutoff that includes some sample on both high and low risks groups.

res.age.60.40 <- separate2GroupsCox(
  chosen.btas = c(age = 1, 0), 
  xdata, 
  ydata, 
  probs = c(.6, .4),
  stop.when.overlap = FALSE
)
## Warning in separate2GroupsCox(chosen.btas = c(age = 1, 0), xdata, ydata, : The cutoff values given to the function allow for some over samples in both groups, with:
##   high risk size (15) + low risk size (16) not equal to xdata/ydata rows (31 != 26)
## 
## We are continuing with execution as parameter stop.when.overlap is FALSE.
##   note: This adds duplicate samples to ydata and xdata xdata

1.4.1 Kaplan-Meier survival results

## Kaplan-Meier results
## Call: survfit(formula = survival::Surv(time, status) ~ group, data = prognostic.index.df)
## 
##            n events median 0.95LCL 0.95UCL
## Low risk  16      5     NA     638      NA
## High risk 15      9    475     353      NA

1.4.2 Plot

A individual is attributed to low-risk group if its calculated relative risk (using Cox Proportional model) is below the median risk.

The opposite for the high-risk groups, populated with individuals above the median relative-risk.

2 Session Info

sessionInfo()
## R Under development (unstable) (2022-10-25 r83175)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.1 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.17-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [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       
## 
## attached base packages:
##  [1] grid      parallel  stats4    stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] VennDiagram_1.7.3           reshape2_1.4.4             
##  [3] forcats_0.5.2               glmSparseNet_1.17.0        
##  [5] glmnet_4.1-4                Matrix_1.5-1               
##  [7] TCGAutils_1.19.0            curatedTCGAData_1.19.2     
##  [9] MultiAssayExperiment_1.25.0 SummarizedExperiment_1.29.0
## [11] Biobase_2.59.0              GenomicRanges_1.51.0       
## [13] GenomeInfoDb_1.35.0         IRanges_2.33.0             
## [15] S4Vectors_0.37.0            BiocGenerics_0.45.0        
## [17] MatrixGenerics_1.11.0       matrixStats_0.62.0         
## [19] futile.logger_1.4.3         survival_3.4-0             
## [21] ggplot2_3.3.6               dplyr_1.0.10               
## [23] BiocStyle_2.27.0           
## 
## loaded via a namespace (and not attached):
##   [1] jsonlite_1.8.3                shape_1.4.6                  
##   [3] magrittr_2.0.3                magick_2.7.3                 
##   [5] GenomicFeatures_1.51.0        farver_2.1.1                 
##   [7] rmarkdown_2.17                BiocIO_1.9.0                 
##   [9] zlibbioc_1.45.0               vctrs_0.5.0                  
##  [11] memoise_2.0.1                 Rsamtools_2.15.0             
##  [13] RCurl_1.98-1.9                rstatix_0.7.0                
##  [15] htmltools_0.5.3               progress_1.2.2               
##  [17] AnnotationHub_3.7.0           lambda.r_1.2.4               
##  [19] curl_4.3.3                    broom_1.0.1                  
##  [21] pROC_1.18.0                   sass_0.4.2                   
##  [23] bslib_0.4.0                   plyr_1.8.7                   
##  [25] zoo_1.8-11                    futile.options_1.0.1         
##  [27] cachem_1.0.6                  GenomicAlignments_1.35.0     
##  [29] mime_0.12                     lifecycle_1.0.3              
##  [31] iterators_1.0.14              pkgconfig_2.0.3              
##  [33] R6_2.5.1                      fastmap_1.1.0                
##  [35] GenomeInfoDbData_1.2.9        shiny_1.7.3                  
##  [37] digest_0.6.30                 colorspace_2.0-3             
##  [39] AnnotationDbi_1.61.0          ExperimentHub_2.7.0          
##  [41] RSQLite_2.2.18                ggpubr_0.4.0                 
##  [43] filelock_1.0.2                labeling_0.4.2               
##  [45] km.ci_0.5-6                   fansi_1.0.3                  
##  [47] abind_1.4-5                   httr_1.4.4                   
##  [49] compiler_4.3.0                bit64_4.0.5                  
##  [51] withr_2.5.0                   backports_1.4.1              
##  [53] BiocParallel_1.33.0           carData_3.0-5                
##  [55] DBI_1.1.3                     highr_0.9                    
##  [57] ggsignif_0.6.4                biomaRt_2.55.0               
##  [59] rappdirs_0.3.3                DelayedArray_0.25.0          
##  [61] rjson_0.2.21                  tools_4.3.0                  
##  [63] interactiveDisplayBase_1.37.0 httpuv_1.6.6                 
##  [65] glue_1.6.2                    restfulr_0.0.15              
##  [67] promises_1.2.0.1              generics_0.1.3               
##  [69] gtable_0.3.1                  KMsurv_0.1-5                 
##  [71] tzdb_0.3.0                    tidyr_1.2.1                  
##  [73] survminer_0.4.9               data.table_1.14.4            
##  [75] hms_1.1.2                     car_3.1-1                    
##  [77] xml2_1.3.3                    utf8_1.2.2                   
##  [79] XVector_0.39.0                BiocVersion_3.17.0           
##  [81] foreach_1.5.2                 pillar_1.8.1                 
##  [83] stringr_1.4.1                 later_1.3.0                  
##  [85] splines_4.3.0                 BiocFileCache_2.7.0          
##  [87] lattice_0.20-45               rtracklayer_1.59.0           
##  [89] bit_4.0.4                     tidyselect_1.2.0             
##  [91] Biostrings_2.67.0             knitr_1.40                   
##  [93] gridExtra_2.3                 bookdown_0.29                
##  [95] xfun_0.34                     stringi_1.7.8                
##  [97] yaml_2.3.6                    evaluate_0.17                
##  [99] codetools_0.2-18              tibble_3.1.8                 
## [101] BiocManager_1.30.19           cli_3.4.1                    
## [103] xtable_1.8-4                  munsell_0.5.0                
## [105] jquerylib_0.1.4               survMisc_0.5.6               
## [107] Rcpp_1.0.9                    GenomicDataCommons_1.23.0    
## [109] dbplyr_2.2.1                  png_0.1-7                    
## [111] XML_3.99-0.12                 ellipsis_0.3.2               
## [113] readr_2.1.3                   assertthat_0.2.1             
## [115] blob_1.2.3                    prettyunits_1.1.1            
## [117] bitops_1.0-7                  scales_1.2.1                 
## [119] purrr_0.3.5                   crayon_1.5.2                 
## [121] rlang_1.0.6                   KEGGREST_1.39.0              
## [123] rvest_1.0.3                   formatR_1.12