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BioMark (version 0.4.5)

Find Biomarkers in Two-Class Discrimination Problems

Description

Variable selection methods are provided for several classification methods: the lasso/elastic net, PCLDA, PLSDA, and several t-tests. Two approaches for selecting cutoffs can be used, one based on the stability of model coefficients under perturbation, and the other on higher criticism.

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Version

Install

install.packages('BioMark')

Monthly Downloads

286

Version

0.4.5

License

GPL (>= 2)

Maintainer

Ron Wehrens

Last Published

September 7th, 2015

Functions in BioMark (0.4.5)

get.biom

Get biomarkers discriminating between two classes
SpikedApple

Spike-in metabolomics data for apple extracts
biom.options

Set or return options for stability-based biomarker selection
aux.biom

Auxiliary functions in the biomarker package
scalefun

Different forms of scaling
HCthresh

Biomarker thresholding by Higher Criticism
spikedApples

Metabolomics data on spiked apples
gen.data

Simulate data sets
traceplot

Plot the coefficient or stability trace for the lasso/elastic net biomarker selection.
get.segments

Subsampling segments
selection

Accessor function to the selected variables of a BioMark object
ROC

ROC curves