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.

Functions

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

Files

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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