MetabolicSurv

A Biomarker Validation Approach for Classification and Predicting Survival Using Metabolomics Signature

v1.1.2 · Jun 11, 2021 · GPL-3

Description

An approach to identifies metabolic biomarker signature for metabolic data by discovering predictive metabolite for predicting survival and classifying patients into risk groups. Classifiers are constructed as a linear combination of predictive/important metabolites, prognostic factors and treatment effects if necessary. Several methods were implemented to reduce the metabolomics matrix such as the principle component analysis of Wold Svante et al. (1987) <doi:10.1016/0169-7439(87)80084-9> , the LASSO method by Robert Tibshirani (1998) <doi:10.1002/(SICI)1097-0258(19970228)16:4%3C385::AID-SIM380%3E3.0.CO;2-3>, the elastic net approach by Hui Zou and Trevor Hastie (2005) <doi:10.1111/j.1467-9868.2005.00503.x>. Sensitivity analysis on the quantile used for the classification can also be accessed to check the deviation of the classification group based on the quantile specified. Large scale cross validation can be performed in order to investigate the mostly selected predictive metabolites and for internal validation. During the evaluation process, validation is accessed using the hazard ratios (HR) distribution of the test set and inference is mainly based on resampling and permutations technique.

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Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	NOTE	168.8s
r-devel-linux-x86_64-debian-gcc	NOTE	117.3s
r-devel-linux-x86_64-fedora-clang	NOTE	271.7s
r-devel-linux-x86_64-fedora-gcc	NOTE	282.8s
r-devel-macos-arm64	NOTE	43s
r-devel-windows-x86_64	NOTE	181s
r-oldrel-macos-arm64	NOTE
r-oldrel-macos-x86_64	NOTE	101s
r-oldrel-windows-x86_64	NOTE	239s
r-patched-linux-x86_64	NOTE	155.2s
r-release-linux-x86_64	NOTE	154.6s
r-release-macos-arm64	NOTE
r-release-macos-x86_64	NOTE	130s
r-release-windows-x86_64	NOTE	178s

Check details (14 non-OK)

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NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026

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checkRd: (-1) CVLasoelacox.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:70-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:74-76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) CVLasoelacox.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:70-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:74-76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) CVLasoelacox.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:70-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:74-76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) CVLasoelacox.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:70-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:74-76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox

Dependency Network

Version History

new 1.1.2 Mar 10, 2026

Maintainer

Olajumoke Evangelina Owokotomo

Dependencies

Depends

R (>= 4.1.0)

Imports

superpc glmnet matrixStats survminer survival rms tidyr pls Rdpack methods stats ggplot2 dplyr

Suggests

knitr rmarkdown

Compilation

No compilation needed

First Published

Mar 10, 2026

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