Package: MetabolicSurv 1.1.0

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.

Authors:Olajumoke Evangelina Owokotomo [aut, cre], Ziv Shkedy [aut]

MetabolicSurv_1.1.0.tar.gz
MetabolicSurv_1.1.0.zip(r-4.5)MetabolicSurv_1.1.0.zip(r-4.4)MetabolicSurv_1.1.0.zip(r-4.3)
MetabolicSurv_1.1.0.tgz(r-4.4-any)MetabolicSurv_1.1.0.tgz(r-4.3-any)
MetabolicSurv_1.1.0.tar.gz(r-4.5-noble)MetabolicSurv_1.1.0.tar.gz(r-4.4-noble)
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MetabolicSurv.pdf |MetabolicSurv.html
MetabolicSurv/json (API)
NEWS

# Install 'MetabolicSurv' in R:
install.packages('MetabolicSurv', repos = c('https://olajumokeevangelina.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/olajumokeevangelina/metabolicsurv/issues

Datasets:
  • DataHR - Survival and Prognostic Data .

On CRAN:

4.13 score 27 scripts 184 downloads 20 exports 136 dependencies

Last updated 5 years agofrom:3cba18aed0. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-winNOTENov 16 2024
R-4.5-linuxNOTENov 16 2024
R-4.4-winNOTENov 16 2024
R-4.4-macNOTENov 16 2024
R-4.3-winNOTEAug 18 2024
R-4.3-macNOTEAug 18 2024

Exports:CVLasoelacoxCVMajorityvotesCVMetSpecificCoxPhCVPcaPlsCVSimDistHREstimateHRIcvlasoelLasoelacoxMajorityvotesMetFreqMSDataMSpecificCoxPhplotQuantileAnalysisshowSIMetsummarySurvPcaClassSurvPlsClass

Dependencies:abindbackportsbase64encbitopsbootbroombslibcachemcarcarDatacaToolscheckmatecliclustercodetoolscolorspacecommonmarkcorrplotcowplotcpp11curldata.tableDerivdigestdoBydplyrevaluateexactRankTestsfansifarverfastmapfontawesomeforeachforeignFormulafsgenericsggplot2ggpubrggrepelggsciggsignifggtextglmnetgluegplotsgridExtragridtextgtablegtoolshighrHmischtmlTablehtmltoolshtmlwidgetsisobanditeratorsjpegjquerylibjsonliteKernSmoothkm.ciKMsurvknitrlabelinglatticelifecyclelme4magrittrmarkdownMASSMatrixMatrixModelsmatrixStatsmaxstatmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompmunsellmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigplspngpolsplinepolynompurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackrlangrmarkdownrmsrpartrstatixrstudioapisandwichsassscalesshapeSparseMstringistringrsuperpcsurvivalsurvminersurvMiscTH.datatibbletidyrtidyselecttinytexutf8vctrsviridisviridisLitewithrxfunxml2xtableyamlzoo

MetabolicSurv: A Biomarker Validation approach for Classification and Predicting Survival Using Metabolomic Signature

Rendered fromMetabolicSurv.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2019-08-06
Started: 2018-10-30

Readme and manuals

Help Manual

Help pageTopics
Cross Validations for Lasso Elastic Net Survival predictive models and ClassificationCVLasoelacox
The cvle Class.cvle cvle-class plot,cvle,missing-method show,cvle-method summary,cvle-method
Cross validation for majority votesCVMajorityvotes
Cross validation for the Metabolite specific analysisCVMetSpecificCoxPh
The cvmm Class.cvmm cvmm-class plot,cvmm,ANY-method show,cvmm-method summary,cvmm-method
The cvmv Class.cvmv cvmv-class plot,cvmv,ANY-method show,cvmv-method summary,cvmv-method
Cross Validations for PCA and PLS based methodsCVPcaPls
The cvpp Class.cvpp cvpp-class plot,cvpp,missing-method show,cvpp-method summary,cvpp-method
Cross validation for sequentially increases metabolitesCVSim
The cvsim Class.cvsim cvsim-class plot,cvsim,missing-method show,cvsim-method summary,cvsim-method
Survival and Prognostic Data .DataHR
Null Distribution of the Estimated HRDistHR
Classification, Survival Estimation and VisualizationEstimateHR
The fcv Class.fcv fcv-class plot,fcv,missing-method show,fcv-method summary,fcv-method
Inner and Outer Cross Validations for Lasso Elastic Net Survival predictive models and ClassificationIcvlasoel
Wapper function for glmnetLasoelacox
Classifiction for Majority VotesMajorityvotes
MetabolicSurv: A biomarker validation approach for predicting survival using metabolic signature.MetabolicSurv-package MetabolicSurv
Frequency of Selected Metabolites from the LASSO, Elastic-net Cross-ValidationMetFreq
The ms Class.ms ms-class plot,ms,ANY-method show,ms-method summary,ms-method
Generate Artificial Metabolic Survival DataMSData
Metabolite by metabolite Cox proportional analysisMSpecificCoxPh
The perm Class.perm perm-class plot,perm,ANY-method show,perm-method summary,perm-method
Quantile sensitivity analysisQuantileAnalysis
Sequential Increase in Metabolites for the PCA or PLS classifierSIMet
Survival PCA and Classification for metabolic dataSurvPcaClass
Survival PLS and Classification for metabolic dataSurvPlsClass