survJamda: Survival Prediction by Joint Analysis of Microarray Gene Expression Data

Microarray gene expression data can be analyzed individually or jointly using merging methods or meta-analysis to predict patients' survival and risk assessment.

AuthorHaleh Yasrebi
Date of publication2015-11-05 20:33:44
MaintainerHaleh Yasrebi<hyasrebi@yahoo.com>
LicenseGPL (>= 2)
Version1.1.4

View on CRAN

Man pages

aprior: Calculate empirical hyper-prior values

Beta.NA: Fit the L/S model in the presence of missing data 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...

calPerformance.merge.indep: Assess performance derived from the merged data set by...

calPerformance.meta: Meta analysis of survival data

calPerformance.single.indep: Performance assessment on single data sets using independent...

ci.gm: Confidence interval of a Geometric mean

ComBat: ComBat-adjusted microarray gene expression data

combat.likelihood: Likelihood function.

comb.surv.censor: Merge survival times and censoring status.

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.

detFileName: Determine the name of a file.

det.set.ind: Determine the indices of the training or testing set.

det.set.meta: Split data for meta analysis.

eval.merge.simulate: Performance evaluation by merging two simulated independent...

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.

iter.crossval: Performance assessment of gene signatures by...

iter.crossval.combat: Merge data set by ComBat within cross-validation.

iter.subset: Performance evaluation by subsetting data sets in 100...

it.sol: Iterative solution for Empirical Bayesian method.

L: Likelihood function.

list.batch: Make a list of data batches.

main.merge.indep.valid: Performance assessment of merged data sets by independent...

main.process: main.process

main.single.indep.valid: Independent validation of the performance of the gene...

meta.main: Meta analysis of survival data.

plotROC: Plot ROC curves related to different time points.

plot.roc.curves: Plot ROC curves of the testing set normalized by a joint...

plot.time.dep: Plot time-dependent ROC curves from 0 to 120 months.

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...

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...

splitZscore2.auc.plot: Z-score2 normalization prior to AUC plot.

splitZscore2.merge.indep: Merge data sets by Z-score2 normalization and assess the...

survJamda-package: Survival Prediction by Joint Analysis of Microarray Gene...

trim.dat: Trim the data.

writeGeno: Reformat gene expression data for ComBat.

writeSamples: Write batch samples for ComBat.

znorm: Matrix Z-score normalization.

Files in this package

survJamda
survJamda/inst
survJamda/inst/citation
survJamda/inst/doc
survJamda/inst/doc/survJamda.R
survJamda/inst/doc/survJamda.Rnw
survJamda/inst/doc/survJamda.pdf
survJamda/NAMESPACE
survJamda/R
survJamda/R/excl.missing.single.indep.R survJamda/R/featureselection.meta.R survJamda/R/main.merge.indep.valid.R survJamda/R/postvar.R survJamda/R/prepzscore2.R survJamda/R/prepcombat.single.indep.R survJamda/R/gm.R survJamda/R/plot.time.dep.R survJamda/R/det.batchID.R survJamda/R/eval.merge.simulate.R survJamda/R/detFileName.R survJamda/R/meta.main.R survJamda/R/it.sol.R survJamda/R/main.single.indep.valid.R survJamda/R/excl.samples.R survJamda/R/prepzscore.R survJamda/R/ComBat.R survJamda/R/det.set.ind.R survJamda/R/filter.absent.R survJamda/R/proc.simulate.R survJamda/R/inv.normal.R survJamda/R/L.R survJamda/R/calPerformance.meta.R survJamda/R/excl.missing.R survJamda/R/aprior.R survJamda/R/cal.cox.coef.R survJamda/R/int.eprior.R survJamda/R/splitZscore2.merge.indep.R survJamda/R/prepcombat.R survJamda/R/main.process.R survJamda/R/iter.crossval.R survJamda/R/groups.cv.R survJamda/R/iter.subset.R survJamda/R/pred.time.indep.valid.R survJamda/R/Beta.NA.R survJamda/R/init.plot.R survJamda/R/splitMerged.auc.plot.R survJamda/R/featureselection.R survJamda/R/design.mat.R survJamda/R/pool.zscores.R survJamda/R/bprior.R survJamda/R/postmean.R survJamda/R/build.design.R survJamda/R/generate.survival.data.R survJamda/R/splitZscore2.auc.plot.R survJamda/R/cross.val.combat.R survJamda/R/comb.surv.censor.R survJamda/R/splitMerged.indep.R survJamda/R/znorm.R survJamda/R/plotROC.R survJamda/R/trim.dat.R survJamda/R/eval.subset.R survJamda/R/det.set.meta.R survJamda/R/calPerformance.auc.plot.R survJamda/R/list.batch.R survJamda/R/shuffle.samples.R survJamda/R/prepzscore1.R survJamda/R/calPerformance.merge.indep.R survJamda/R/calPerformance.single.indep.R survJamda/R/ci.gm.R survJamda/R/iter.crossval.combat.R survJamda/R/writeSamples.R survJamda/R/cross.val.surv.R survJamda/R/plot.roc.curves.R survJamda/R/combat.likelihood.R survJamda/R/compute.combat.R survJamda/R/writeGeno.R
survJamda/vignettes
survJamda/vignettes/survJamda.Rnw
survJamda/vignettes/predictTime.png
survJamda/vignettes/AUC10fCVgse43351gn.png
survJamda/MD5
survJamda/build
survJamda/build/vignette.rds
survJamda/DESCRIPTION
survJamda/man
survJamda/man/calPerformance.merge.indep.Rd survJamda/man/iter.crossval.combat.Rd survJamda/man/detFileName.Rd survJamda/man/trim.dat.Rd survJamda/man/calPerformance.meta.Rd survJamda/man/plot.roc.curves.Rd survJamda/man/list.batch.Rd survJamda/man/cross.val.surv.Rd survJamda/man/compute.combat.Rd survJamda/man/prepzscore2.Rd survJamda/man/build.design.Rd survJamda/man/postmean.Rd survJamda/man/main.single.indep.valid.Rd survJamda/man/cross.val.combat.Rd survJamda/man/excl.missing.Rd survJamda/man/prepzscore.Rd survJamda/man/eval.subset.Rd survJamda/man/featureselection.meta.Rd survJamda/man/Beta.NA.Rd survJamda/man/design.mat.Rd survJamda/man/iter.crossval.Rd survJamda/man/meta.main.Rd survJamda/man/bprior.Rd survJamda/man/main.merge.indep.valid.Rd survJamda/man/iter.subset.Rd survJamda/man/prepcombat.Rd survJamda/man/calPerformance.auc.plot.Rd survJamda/man/excl.samples.Rd survJamda/man/ci.gm.Rd survJamda/man/generate.survival.data.Rd survJamda/man/pred.time.indep.valid.Rd survJamda/man/det.set.meta.Rd survJamda/man/groups.cv.Rd survJamda/man/writeGeno.Rd survJamda/man/pool.zscores.Rd survJamda/man/splitMerged.indep.Rd survJamda/man/splitZscore2.merge.indep.Rd survJamda/man/cal.cox.coef.Rd survJamda/man/plotROC.Rd survJamda/man/znorm.Rd survJamda/man/prepcombat.single.indep.Rd survJamda/man/combat.likelihood.Rd survJamda/man/survJamda-package.Rd survJamda/man/featureselection.Rd survJamda/man/comb.surv.censor.Rd survJamda/man/init.plot.Rd survJamda/man/splitMerged.auc.plot.Rd survJamda/man/prepzscore1.Rd survJamda/man/splitZscore2.auc.plot.Rd survJamda/man/det.set.ind.Rd survJamda/man/proc.simulate.Rd survJamda/man/L.Rd survJamda/man/it.sol.Rd survJamda/man/postvar.Rd survJamda/man/calPerformance.single.indep.Rd survJamda/man/gm.Rd survJamda/man/filter.absent.Rd survJamda/man/shuffle.samples.Rd survJamda/man/excl.missing.single.indep.Rd survJamda/man/plot.time.dep.Rd survJamda/man/int.eprior.Rd survJamda/man/ComBat.Rd survJamda/man/main.process.Rd survJamda/man/writeSamples.Rd survJamda/man/aprior.Rd survJamda/man/det.batchID.Rd survJamda/man/eval.merge.simulate.Rd survJamda/man/inv.normal.Rd

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