Find Biomarkers in Two-Class Discrimination Problems

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.


0.4.2: - updated maintainers' email address - fixed NAMESPACE issues - changed the way global options are handled

0.4.1: - updated citation information: an appropriate reference for the software package is now available, rather than a reference to the first paper in which the package was used.

0.4.0: - added lasso and elastic nets to the list of methods for "coef" and "stab"; also changes in biom.options and get.biom. Additional function traceplot. - return values for auxiliary functions like studentt.stab and friends have changed: now they only contain (corrected) frequencies in which a particular variable is among the ntop best variables. Also the names have changed: coef.size now is only returned when type == "coef" - coef.BMark function no longer returns indices of selected variables but coefficient sizes when type == "coef" (this was already the case), selection frequencies for stability selection, and estimated p values for HC thresholding. - added "selection" function to get the selected variables - the input of the get.biom function is changed: for classification cases Y must be a factor. If a numerical vector is used for Y with only two different values, it is converted into a factor with a warning. - output of the get.biom function is organized differently: now the top level of the list consists of the different methods (studentt, vip, lasso), and the second level consists of the different parameter settings for each method (lambda for lasso, ncomp for plsda/pclda/vip). - now also support for regression in stability selection. As a result, naming of fmethods has changed: "plsda" and "pclda" are now replaced by "pls" and "pcr", respectively. The old names still work but give a warning. - updated references (once again) - several corrections to man pages (in biom.options, get.biom); spotted by Nir Shahaf.

0.3.3: - corrected a bug in biom.options()

0.3.2: - added NAMESPACE - updated references

0.3.1: - added HCalpha to the options so that HCthresh can be used in get.biom with different alpha values

0.3.0: - all pls methods now use widekernelpls rather than kernelpls - more efficient HC calculations for the multivariate methods, in particular a more efficient p-value estimation - eliminated function since the original in the st package no longer has the verbose output - introduction of BMark object type and the coef, print and summary generic functions - simplification of get.biom function argument list by definition of biom.options function and .biom.options object, as in the pls package - default values for stability-based selection are now the ones used in the 2011 ACA paper, in particular the default for scaling now is "auto" and no longer "none" - renaming of all foo.biom functions to foo.stab - implementation of Higher Criticism

0.2.6: first version submitted to CRAN, and used in the 2011 ACA publication

Reference manual

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0.4.5 by Ron Wehrens, 4 years ago

Browse source code at

Authors: Ron Wehrens , Pietro Franceschi

Documentation:   PDF Manual  

Task views: Chemometrics and Computational Physics

GPL (>= 2) license

Depends on pls, glmnet, MASS, st

See at CRAN