Man pages for survJamda
Survival Prediction by Joint Analysis of Microarray Gene Expression Data

apriorCalculate empirical hyper-prior values
Beta.NAFit the L/S model in the presence of missing data values
bpriorCalculate empirical hyper-prior values of Bayesian model
build.designInitiation to build the design matrix
cal.cox.coefCox coefficient calculation.
calPerformance.auc.plotAssess the performance obtained from the merged data set by...
calPerformance.merge.indepAssess performance derived from the merged data set by...
calPerformance.metaMeta analysis of survival data
calPerformance.single.indepPerformance assessment on single data sets using independent...
ci.gmConfidence interval of a Geometric mean
ComBatComBat-adjusted microarray gene expression data
combat.likelihoodLikelihood function.
comb.surv.censorMerge survival times and censoring status.
compute.combatInitiate ComBat adjustment
cross.val.combatCross validation with ComBat adjustment
cross.val.survCross validation with or without Z-score normalization
design.matBuild a design matrix
det.batchIDDetermine the batch ID of data sets.
detFileNameDetermine the name of a file.
det.set.indDetermine the indices of the training or testing set.
det.set.metaSplit data for meta analysis.
eval.merge.simulatePerformance evaluation by merging two simulated independent...
eval.subsetPerformance evaluation derived from a subset of a data set
excl.missingExclude missing samples
excl.missing.single.indepExclude missing samples prior to independent validation
excl.samplesExclude samples
featureselectionApply a feature selection
featureselection.metaFeature selection for meta analysis
filter.absentFilter absent calls
generate.survival.dataGenerate survival data.
gmGeometric Mean
groups.cvSplit a data set for cross-validation
init.plotStart plotting
int.epriorIntegration function to find nonparametric adjustments
inv.normalApply the inverse normal method.
iter.crossvalPerformance assessment of gene signatures by...
iter.crossval.combatMerge data set by ComBat within cross-validation.
iter.subsetPerformance evaluation by subsetting data sets in 100...
it.solIterative solution for Empirical Bayesian method.
LLikelihood function.
list.batchMake a list of data batches.
main.merge.indep.validPerformance assessment of merged data sets by independent...
main.single.indep.validIndependent validation of the performance of the gene...
meta.mainMeta analysis of survival data.
plotROCPlot ROC curves related to different time points.
plot.roc.curvesPlot ROC curves of the testing set normalized by a joint...
plot.time.depPlot time-dependent ROC curves from 0 to 120 months.
pool.zscoresCombine data for meta analysis.
postmeanEstimated additive batch effect
postvarEstimated multiplicative batch effect
pred.time.indep.validPrediction of survival time by independent validation.
prepcombatCombination of data sets prior to the application of ComBat.
prepcombat.single.indepPair-wise combination of single data sets prior to the...
prepzscoreZ-score normalization.
prepzscore1Apply Z-score1 normalization.
prepzscore2Apply Z-score2 normalization.
proc.simulateSimulate survival data.
shuffle.samplesShuffle samples.
splitMerged.auc.plotDetermine the indices of the training and testing sets.
splitMerged.indepMerge the data sets by ComBat or Z-score1 normalization and...
splitZscore2.auc.plotZ-score2 normalization prior to AUC plot.
splitZscore2.merge.indepMerge data sets by Z-score2 normalization and assess the...
survJamda-packageSurvival Prediction by Joint Analysis of Microarray Gene...
trim.datTrim the data.
writeGenoReformat gene expression data for ComBat.
writeSamplesWrite batch samples for ComBat.
znormMatrix Z-score normalization.
survJamda documentation built on May 1, 2019, 8:50 p.m.