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

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.

Version: 1.1.0
Depends: R (≥ 3.1.0)
Imports: superpc, glmnet, matrixStats, survminer, survival, rms, tidyr, pls, Rdpack, methods, stats, gplots, ggplot2
Suggests: knitr, rmarkdown
Published: 2019-08-05
Author: Olajumoke Evangelina Owokotomo [aut, cre], Ziv Shkedy [aut]
Maintainer: Olajumoke Evangelina Owokotomo <olajumoke.owokotomo at uhasselt.be>
BugReports: https://github.com/OlajumokeEvangelina/MetabolicSurv/issues/new
License: GPL-3
URL: https://github.com/OlajumokeEvangelina/MetabolicSurv
NeedsCompilation: no
Materials: README NEWS
CRAN checks: MetabolicSurv results

Downloads:

Reference manual: MetabolicSurv.pdf
Vignettes: MetabolicSurv: A Biomarker Validation approach for Classification and Predicting Survival Using Metabolomic Signature
Package source: MetabolicSurv_1.1.0.tar.gz
Windows binaries: r-devel: MetabolicSurv_1.1.0.zip, r-release: MetabolicSurv_1.1.0.zip, r-oldrel: MetabolicSurv_1.1.0.zip
OS X binaries: r-release: MetabolicSurv_1.1.0.tgz, r-oldrel: MetabolicSurv_1.1.0.tgz
Old sources: MetabolicSurv archive

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