Separate 2 groups in Cox regression
2025-10-30
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
flog.layout(layout.format("[~l] ~m"))
options("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)
resAge <- separate2GroupsCox(c(age = 1, 0), xdata, ydata)1.2.1 Kaplan-Meier survival results
## Call: survfit(formula = survival::Surv(time, status) ~ group, data = prognosticIndexDf)
##
## n events median 0.95LCL 0.95UCL
## Low risk - 1 13 4 NA 638 NA
## High risk - 1 13 8 464 268 NA1.2.2 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%)
resAge4060 <-
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 = prognosticIndexDf)
##
## n events median 0.95LCL 0.95UCL
## Low risk - 1 11 3 NA 563 NA
## High risk - 1 10 7 359 156 NA1.3.2 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.
resAge6040 <- separate2GroupsCox(
chosenBetas = c(age = 1, 0),
xdata,
ydata,
probs = c(.6, .4),
stopWhenOverlap = FALSE
)## Warning in buildPrognosticIndexDataFrame(ydata, probs, stopWhenOverlap, : 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 `stopWhenOverlap` is FALSE.
## note: This adds duplicate samples to ydata and xdata xdata1.4.1 Kaplan-Meier survival results
## Kaplan-Meier results## Call: survfit(formula = survival::Surv(time, status) ~ group, data = prognosticIndexDf)
##
## n events median 0.95LCL 0.95UCL
## Low risk - 1 16 5 NA 638 NA
## High risk - 1 15 9 475 353 NA1.4.2 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 version 4.5.1 Patched (2025-08-23 r88802)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
##
## 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
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] grid parallel stats4 stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] glmnet_4.1-10 VennDiagram_1.7.3
## [3] reshape2_1.4.4 forcats_1.0.1
## [5] Matrix_1.7-4 glmSparseNet_1.28.0
## [7] TCGAutils_1.30.0 curatedTCGAData_1.31.3
## [9] MultiAssayExperiment_1.36.0 SummarizedExperiment_1.40.0
## [11] Biobase_2.70.0 GenomicRanges_1.62.0
## [13] Seqinfo_1.0.0 IRanges_2.44.0
## [15] S4Vectors_0.48.0 BiocGenerics_0.56.0
## [17] generics_0.1.4 MatrixGenerics_1.22.0
## [19] matrixStats_1.5.0 futile.logger_1.4.3
## [21] survival_3.8-3 ggplot2_4.0.0
## [23] dplyr_1.1.4 BiocStyle_2.38.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 jsonlite_2.0.0
## [3] shape_1.4.6.1 magrittr_2.0.4
## [5] magick_2.9.0 GenomicFeatures_1.62.0
## [7] farver_2.1.2 rmarkdown_2.30
## [9] BiocIO_1.20.0 vctrs_0.6.5
## [11] memoise_2.0.1 Rsamtools_2.26.0
## [13] RCurl_1.98-1.17 rstatix_0.7.3
## [15] tinytex_0.57 htmltools_0.5.8.1
## [17] S4Arrays_1.10.0 BiocBaseUtils_1.12.0
## [19] progress_1.2.3 AnnotationHub_4.0.0
## [21] lambda.r_1.2.4 curl_7.0.0
## [23] broom_1.0.10 Formula_1.2-5
## [25] pROC_1.19.0.1 SparseArray_1.10.0
## [27] sass_0.4.10 bslib_0.9.0
## [29] plyr_1.8.9 httr2_1.2.1
## [31] zoo_1.8-14 futile.options_1.0.1
## [33] cachem_1.1.0 GenomicAlignments_1.46.0
## [35] lifecycle_1.0.4 iterators_1.0.14
## [37] pkgconfig_2.0.3 R6_2.6.1
## [39] fastmap_1.2.0 digest_0.6.37
## [41] AnnotationDbi_1.72.0 ps_1.9.1
## [43] ExperimentHub_3.0.0 RSQLite_2.4.3
## [45] ggpubr_0.6.2 labeling_0.4.3
## [47] filelock_1.0.3 km.ci_0.5-6
## [49] httr_1.4.7 abind_1.4-8
## [51] compiler_4.5.1 bit64_4.6.0-1
## [53] withr_3.0.2 S7_0.2.0
## [55] backports_1.5.0 BiocParallel_1.44.0
## [57] carData_3.0-5 DBI_1.2.3
## [59] ggsignif_0.6.4 biomaRt_2.66.0
## [61] rappdirs_0.3.3 DelayedArray_0.36.0
## [63] rjson_0.2.23 tools_4.5.1
## [65] chromote_0.5.1 otel_0.2.0
## [67] glue_1.8.0 restfulr_0.0.16
## [69] promises_1.4.0 checkmate_2.3.3
## [71] gtable_0.3.6 KMsurv_0.1-6
## [73] tzdb_0.5.0 tidyr_1.3.1
## [75] survminer_0.5.1 websocket_1.4.4
## [77] data.table_1.17.8 hms_1.1.4
## [79] car_3.1-3 xml2_1.4.1
## [81] XVector_0.50.0 BiocVersion_3.22.0
## [83] foreach_1.5.2 pillar_1.11.1
## [85] stringr_1.5.2 later_1.4.4
## [87] splines_4.5.1 BiocFileCache_3.0.0
## [89] lattice_0.22-7 rtracklayer_1.70.0
## [91] bit_4.6.0 tidyselect_1.2.1
## [93] Biostrings_2.78.0 knitr_1.50
## [95] gridExtra_2.3 bookdown_0.45
## [97] xfun_0.53 stringi_1.8.7
## [99] UCSC.utils_1.6.0 yaml_2.3.10
## [101] evaluate_1.0.5 codetools_0.2-20
## [103] cigarillo_1.0.0 tibble_3.3.0
## [105] BiocManager_1.30.26 cli_3.6.5
## [107] xtable_1.8-4 processx_3.8.6
## [109] jquerylib_0.1.4 survMisc_0.5.6
## [111] dichromat_2.0-0.1 Rcpp_1.1.0
## [113] GenomeInfoDb_1.46.0 GenomicDataCommons_1.34.0
## [115] dbplyr_2.5.1 png_0.1-8
## [117] XML_3.99-0.19 readr_2.1.5
## [119] blob_1.2.4 prettyunits_1.2.0
## [121] bitops_1.0-9 scales_1.4.0
## [123] purrr_1.1.0 crayon_1.5.3
## [125] rlang_1.1.6 KEGGREST_1.50.0
## [127] rvest_1.0.5 formatR_1.14