iterativeBMA (version 1.30.0)

iterateBMAsurv.train.predict.assess: Iterative Bayesian Model Averaging: training, prediction, assessment

Description

Survival analysis and variable selection on microarray data. This is a multivariate technique to select a small number of relevant variables (typically genes) to perform survival analysis on microarray data. This function performs the training, prediction, and assessment steps. The data is not assumed to be pre-sorted by rank before this function is called.

Usage

iterateBMAsurv.train.predict.assess (train.dat, test.dat, surv.time.train, surv.time.test, cens.vec.train, cens.vec.test, p=100, nbest=10, maxNvar=25, maxIter=200000, thresProbne0=1, cutPoint=50, verbose = FALSE, suff.string="")

Arguments

train.dat

Data matrix for the training set where columns are variables and rows are observations. In the case of gene expression data, the columns (variables) represent genes, while the rows (observations) represent samples. If Cox Proportional Hazards Regression is the desired univariate ranking measure, the data does not need to be pre-sorted. To use a different univariate ranking measure, see iterateBMAsurv.train.wrapper.

test.dat

Data matrix for the test set where columns are variables and rows are observations. In the case of gene expression data, the columns (variables) represent genes, while the rows (observations) represent samples. The test set should contain the same variables as the training set.

surv.time.train

Vector of survival times for the patient samples in the training set. Survival times are assumed to be presented in uniform format (e.g., months or days), and the length of this vector should be equal to the number of rows in train.dat.

surv.time.test

Vector of survival times for the patient samples in the test set. Survival times are assumed to be presented in uniform format (e.g., months or days), and the length of this vector should be equal to the number of rows in test.dat.

cens.vec.train

Vector of censor data for the patient samples in the training set. In general, 0 = censored and 1 = uncensored. The length of this vector should equal the number of rows in train.dat and the number of elements in surv.time.train.

cens.vec.test

Vector of censor data for the patient samples in the test set. In general, 0 = censored and 1 = uncensored. The length of this vector should equal the number of rows in train.dat and the number of elements in surv.time.test.

p

A number indicating the maximum number of top univariate genes used in the iterative bic.surv algorithm. This number is assumed to be less than the total number of genes in the training data. A larger p usually requires longer computational time as more iterations of the bic.surv algorithm are potentially applied. The default is 100.

nbest

A number specifying the number of models of each size returned to bic.surv in the BMA package. The default is 10.

maxNvar

A number indicating the maximum number of variables used in each iteration of bic.surv from the BMA package. The default is 25.

maxIter

A number indicating the maximum iterations of bic.surv. The default is 200000.

thresProbne0

A number specifying the threshold for the posterior probability that each variable (gene) is non-zero (in percent). Variables (genes) with such posterior probability less than this threshold are dropped in the iterative application of bic.surv. The default is 1 percent.

cutPoint

Threshold percent for separating high- from low-risk groups. The default is 50.

verbose

A boolean variable indicating whether or not to print interim information to the console. The default is FALSE.

suff.string

A string for writing to file.

Value

• If all samples are assigned to a single risk group or all samples are in the same censor category, an error message is printed and a boolean variable success is returned as FALSE.If both risk groups are present in the patient test samples, a Kaplan-Meier Survival Analysis Curve is written to file, and a list with 6 components is returned:
• nvar
  The number of variables selected by the last iteration of bic.surv.
• nmodel
  The number of models selected by the last iteration of bic.surv.
• ypred
  The predicted risk scores on the test samples.
• result.table
  A 2 x 2 table indicating the number of test samples in each category (high-risk/censored, high-risk/uncensored, low-risk/censored, low-risk/uncensored).
• statistics
  An object of class survdiff that contains the statistics from survival analysis, including the variance matrix, chi-square statistic, and p-value.
• success
  A boolean variable returned as TRUE if both risk groups are present in the patient test samples.

Details

This function consists of the training phase, the prediction phase, and the assessment phase. The training phase first orders all the variables (genes) by a univariate measure called Cox Proportional Hazards Regression, and then iteratively applies the bic.surv algorithm from the BMA package. The prediction phase uses the variables (genes) selected in the training phase to predict the risk scores of the patient samples in the test set. In the assessment phase, the risk scores are used to designate each test sample as either high-risk or low-risk based on the user-designated cutPoint. Prediction accuracy is measured by the p-value difference between groups as calculated through the central chi-square distribution. In addition, a Kaplan-Meier Survival Analysis Curve illustrating the difference between risk groups is written to file in the working R directory. If Cox Proportional Hazards Regression is the desired univariate ranking algorithm, then calling this function with the training and testing sets is all that is necessary for a complete survival analysis run.

References

Annest, A., Yeung, K.Y., Bumgarner, R.E., and Raftery, A.E. (2008). Iterative Bayesian Model Averaging for Survival Analysis. Manuscript in Progress.

Raftery, A.E. (1995). Bayesian model selection in social research (with Discussion). Sociological Methodology 1995 (Peter V. Marsden, ed.), pp. 111-196, Cambridge, Mass.: Blackwells.

Volinsky, C., Madigan, D., Raftery, A., and Kronmal, R. (1997) Bayesian Model Averaging in Proprtional Hazard Models: Assessing the Risk of a Stroke. Applied Statistics 46: 433-448.

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.

See Also

iterateBMAsurv.train.wrapper, iterateBMAsurv.train, singleGeneCoxph, predictBicSurv, predictiveAssessCategory, trainData, trainSurv, trainCens, testData, testSurv, testCens

Examples

library (BMA)
library(iterativeBMAsurv)
data(trainData)
data(trainSurv)
data(trainCens)
data(testData)
data(testSurv)
data(testCens)

## Use p=10 genes and nbest=5 for fast computation
ret.bma <- iterateBMAsurv.train.predict.assess (train.dat=trainData, test.dat=testData, surv.time.train=trainSurv, surv.time.test=testSurv, cens.vec.train=trainCens, cens.vec.test=testCens, p=10, nbest=5)

## Extract the statistics from this survival analysis run
number.genes <- ret.bma$nvar
number.models <- ret.bma$nmodel
evaluate.success <- ret.bma$statistics