The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402).
|License:||GPL version 2 or higher|
iterateBMAglm.train selects relevant variables by
iteratively applying the
bic.glm function from the
The data is assumed to consist of two classes.
iterateBMAglm.train.predict combines the training
and prediction phases, and returns the predicted posterior probabilities
that each test sample belongs to class 1.
iterateBMAglm.train.predict.test combines the training,
prediction and test phases, and returns a list consisting of the
numbers of selected genes and models using the training data, the number
of classification errors and the Brier Score on the test set.
Ka Yee Yeung, University of Washington, Seattle, WA, with contributions from Adrian Raftery and Ian Painter
Maintainer: Ka Yee Yeung <email@example.com>
Yeung, K.Y., Bumgarner, R.E. and Raftery, A.E. (2005) Bayesian Model Averaging: Development of an improved multi-class, gene selection and classification tool for microarray data. Bioinformatics 21: 2394-2402.
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library (Biobase) library (BMA) library (iterativeBMA) data(trainData) data(trainClass) ## training phase: select relevant genes ret.bic.glm <- iterateBMAglm.train (train.expr.set=trainData, trainClass, p=100) ## get the selected genes with probne0 > 0 ret.gene.names <- ret.bic.glm$namesx[ret.bic.glm$probne0 > 0] data (testData) ## get the subset of test data with the genes from the last iteration of bic.glm curr.test.dat <- t(exprs(testData)[ret.gene.names,]) ## to compute the predicted probabilities for the test samples y.pred.test <- apply (curr.test.dat, 1, bma.predict, postprobArr=ret.bic.glm$postprob, mleArr=ret.bic.glm$mle) ## compute the Brier Score if the class labels of the test samples are known data (testClass) brier.score (y.pred.test, testClass)
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