Beta.NA                 Fit the L/S model in the presence of missing
                        data values
ComBat                  ComBat-adjusted microarray gene expression data
L                       Likelihood function.
aprior                  Calculate empirical hyper-prior values
bprior                  Calculate empirical hyper-prior values of
                        Bayesian model
build.design            Initiation to build the design matrix
cal.cox.coef            Cox coefficient calculation.
calPerformance.auc.plot
                        Assess the performance obtained from the merged
                        data set by independent validation
calPerformance.merge.indep
                        Assess performance derived from the merged data
                        set by independent validation
calPerformance.meta     Meta analysis of survival data
calPerformance.single.indep
                        Performance assessment on single data sets
                        using independent validation
ci.gm                   Confidence interval of a Geometric mean
comb.surv.censor        Merge survival times and censoring status.
combat.likelihood       Likelihood function.
compute.combat          Initiate ComBat adjustment
cross.val.combat        Cross validation with ComBat adjustment
cross.val.surv          Cross validation with or without Z-score
                        normalization
design.mat              Build a design matrix
det.batchID             Determine the batch ID of data sets.
det.set.ind             Determine the indices of the training or
                        testing set.
det.set.meta            Split data for meta analysis.
detFileName             Determine the name of a file.
eval.merge.simulate     Performance evaluation by merging two simulated
                        independent data sets
eval.subset             Performance evaluation derived from a subset of
                        a data set
excl.missing            Exclude missing samples
excl.missing.single.indep
                        Exclude missing samples prior to independent
                        validation
excl.samples            Exclude samples
featureselection        Apply a feature selection
featureselection.meta   Feature selection for meta analysis
filter.absent           Filter absent calls
generate.survival.data
                        Generate survival data.
gm                      Geometric Mean
groups.cv               Split a data set for cross-validation
init.plot               Start plotting
int.eprior              Integration function to find nonparametric
                        adjustments
inv.normal              Apply the inverse normal method.
it.sol                  Iterative solution for Empirical Bayesian
                        method.
iter.crossval           Performance assessment of gene signatures by
                        cross-validation.
iter.crossval.combat    Merge data set by ComBat within
                        cross-validation.
iter.subset             Performance evaluation by subsetting data sets
                        in 100 iterations
list.batch              Make a list of data batches.
main.merge.indep.valid
                        Performance assessment of merged data sets by
                        independent validation
main.process            main.process
main.single.indep.valid
                        Independent validation of the performance of
                        the gene signatures derived from single data
                        sets.
meta.main               Meta analysis of survival data.
plot.roc.curves         Plot ROC curves of the testing set normalized
                        by a joint analysis method.
plot.time.dep           Plot time-dependent ROC curves from 0 to 120
                        months.
plotROC                 Plot ROC curves related to different time
                        points.
pool.zscores            Combine data for meta analysis.
postmean                Estimated additive batch effect
postvar                 Estimated multiplicative batch effect
pred.time.indep.valid   Prediction of survival time by independent
                        validation.
prepcombat              Combination of data sets prior to the
                        application of ComBat.
prepcombat.single.indep
                        Pair-wise combination of single data sets prior
                        to the application of ComBat and independent
                        validation.
prepzscore              Z-score normalization.
prepzscore1             Apply Z-score1 normalization.
prepzscore2             Apply Z-score2 normalization.
proc.simulate           Simulate survival data.
shuffle.samples         Shuffle samples.
splitMerged.auc.plot    Determine the indices of the training and
                        testing sets.
splitMerged.indep       Merge the data sets by ComBat or Z-score1
                        normalization and apply independent validation.
splitZscore2.auc.plot   Z-score2 normalization prior to AUC plot.
splitZscore2.merge.indep
                        Merge data sets by Z-score2 normalization and
                        assess the performance by independent
                        validation.
survJamda-package       Survival Prediction by Joint Analysis of
                        Microarray Gene Expression Data
trim.dat                Trim the data.
writeGeno               Reformat gene expression data for ComBat.
writeSamples            Write batch samples for ComBat.
znorm                   Matrix Z-score normalization.
