Package: MetabolicSurv
Type: Package
Title: A Biomarker Validation Approach for Classification and
        Predicting Survival Using Metabolomics Signature
Version: 1.1.2
Authors@R: c(
       person("Olajumoke Evangelina","Owokotomo",email="olajumoke.owokotomo@uhasselt.be",role=c("aut","cre")),
       person("Ziv","Shkedy",email="ziv.shkedy@uhasselt.be",role="ctb"))
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.
URL: https://github.com/OlajumokeEvangelina/MetabolicSurv
BugReports: https://github.com/OlajumokeEvangelina/MetabolicSurv/issues/new
Depends: R (>= 4.1.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: superpc, glmnet, matrixStats, survminer, survival, rms, tidyr,
        pls, Rdpack, methods, stats, ggplot2, dplyr
RoxygenNote: 7.1.1
RdMacros: Rdpack
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-06-10 22:12:49 UTC; lucp9546
Author: Olajumoke Evangelina Owokotomo [aut, cre],
  Ziv Shkedy [ctb]
Maintainer: Olajumoke Evangelina Owokotomo <olajumoke.owokotomo@uhasselt.be>
Repository: CRAN
Date/Publication: 2021-06-11 08:30:02 UTC
Built: R 4.6.0; ; 2026-04-25 14:17:30 UTC; unix
