Separate 2 groups in Cox regression
2024-04-19
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 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.19-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
##
## 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_4.1-8 VennDiagram_1.7.3
## [3] reshape2_1.4.4 forcats_1.0.0
## [5] Matrix_1.7-0 glmSparseNet_1.21.2
## [7] TCGAutils_1.23.4 curatedTCGAData_1.25.4
## [9] MultiAssayExperiment_1.29.1 SummarizedExperiment_1.33.3
## [11] Biobase_2.63.1 GenomicRanges_1.55.4
## [13] GenomeInfoDb_1.39.14 IRanges_2.37.1
## [15] S4Vectors_0.41.6 BiocGenerics_0.49.1
## [17] MatrixGenerics_1.15.1 matrixStats_1.3.0
## [19] futile.logger_1.4.3 survival_3.5-8
## [21] ggplot2_3.5.0 dplyr_1.1.4
## [23] BiocStyle_2.31.0
##
## loaded via a namespace (and not attached):
## [1] jsonlite_1.8.8 shape_1.4.6.1
## [3] magrittr_2.0.3 magick_2.8.3
## [5] GenomicFeatures_1.55.4 farver_2.1.1
## [7] rmarkdown_2.26 BiocIO_1.13.0
## [9] zlibbioc_1.49.3 vctrs_0.6.5
## [11] memoise_2.0.1 Rsamtools_2.19.4
## [13] RCurl_1.98-1.14 rstatix_0.7.2
## [15] tinytex_0.50 progress_1.2.3
## [17] htmltools_0.5.8.1 S4Arrays_1.3.7
## [19] BiocBaseUtils_1.5.1 AnnotationHub_3.11.5
## [21] lambda.r_1.2.4 curl_5.2.1
## [23] broom_1.0.5 pROC_1.18.5
## [25] SparseArray_1.3.5 sass_0.4.9
## [27] bslib_0.7.0 plyr_1.8.9
## [29] httr2_1.0.1 zoo_1.8-12
## [31] futile.options_1.0.1 cachem_1.0.8
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## [55] bit64_4.0.5 withr_3.0.0
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## [59] carData_3.0-5 DBI_1.2.2
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## [107] tibble_3.2.1 BiocManager_1.30.22
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