BioMark: Find Biomarkers in Two-Class Discrimination Problems

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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.

Author
Ron Wehrens, Pietro Franceschi
Date of publication
2015-09-07 18:17:37
Maintainer
Ron Wehrens <ron.wehrens@gmail.com>
License
GPL (>= 2)
Version
0.4.5

View on CRAN

Man pages

auxBiom
Auxiliary functions in the biomarker package
biom.options
Set or return options for stability-based biomarker selection
gen.data
Simulate data sets
get.biom
Get biomarkers discriminating between two classes
get.segments
Subsampling segments
HCthresh
Biomarker thresholding by Higher Criticism
ROC
ROC curves
scalefun
Different forms of scaling
selection
Accessor function to the selected variables of a BioMark...
SpikedApple
Spike-in metabolomics data for apple extracts
spikedApples
Metabolomics data on spiked apples
traceplot
Plot the coefficient or stability trace for the lasso/elastic...

Files in this package

BioMark
BioMark/TODO
BioMark/inst
BioMark/inst/CITATION
BioMark/NAMESPACE
BioMark/NEWS
BioMark/data
BioMark/data/spikedApples.RData
BioMark/data/SpikeNeg.RData
BioMark/data/SpikePos.RData
BioMark/R
BioMark/R/scale.R
BioMark/R/biom.options.R
BioMark/R/gen.data.R
BioMark/R/biom.HC.R
BioMark/R/biom.coef.R
BioMark/R/segments.R
BioMark/R/roc.R
BioMark/R/get.biom.R
BioMark/R/biom.stab.R
BioMark/MD5
BioMark/DESCRIPTION
BioMark/man
BioMark/man/traceplot.Rd
BioMark/man/gen.data.Rd
BioMark/man/HCthresh.Rd
BioMark/man/get.biom.Rd
BioMark/man/biom.options.Rd
BioMark/man/selection.Rd
BioMark/man/spikedApples.Rd
BioMark/man/ROC.Rd
BioMark/man/get.segments.Rd
BioMark/man/auxBiom.Rd
BioMark/man/SpikedApple.Rd
BioMark/man/scalefun.Rd