cvmm

A 3-way array, The first dimension is the number of metabolites, the second dimension is the HR statistics for the low risk group in the train dataset (HR,1/HR LCI, UCI) while the third dimension is the number of cross validation performed.

HRTrain

A 3-way array, The first dimension is the number of metabolites,
the second dimension is the HR statistics for the low risk group in the test
dataset (HR,1/HR LCI, UCI) while the third dimension is the number of
cross validation performed.

HRTest

The selected subjects for each CV in the train dataset

train

The selected subjects for each CV in the test dataset

test

The number of metabolite used in the analysis

n.mets

The number of cross validation performed

The Metabolite data matrix that was used for the analysis either
same as Mdata or a reduced version

Rdata

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.

cvmm: Constructor for the cvmm class

Description

Usage

Arguments

Value