Man pages for XDE
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression

burninIndicator for running a MCMC burnin
calculatePosteriorAvgCalculate the posterior average for indicators of concordant...
empiricalStartEmpirical starting values for the MCMC
expressionSetListExample of ExpressionSetList
ExpressionSetList-classA class for containing a list of ExpressionSets
ExpressionSetList-methodsMethods for ExpressionSetList
firstMcmcValues for the first MCMC iteration
geneCenterCenter the expression values for each gene in a study to zero
hyperparametersAccessor for hyperparameters of the Bayesian model
iterationsNumber of MCMC iterations
lastMcmcMCMC values for the last iteration
outputOptions for storing results of the MCMC chains
pairspairs function for high-throughput data
Parameters-classContainer for XDE parameters
posteriorAvgAccessor and replacement methods for posterior averages of...
seedSeed for the MCMC
ssStatisticCalculate single study estimates of effect size
standardizeSamplesCenters the genes at zero and standardizes the samples to...
studyCenterCenter the expression values in a study to zero
symbolsInterestingUseful for changing the look of pairs plots to emphasize...
thinHow often to write MCMC iterations to file
tuningTuning parameters for Metropolis-Hastings proposals
updatesFrequency of updating a parameter per MCMC iteration
xdeFit the Bayesian hierarchical model for cross-study...
XdeMcmc-classClass for storing output from the Bayesian model
XdeParameter-classContainer class for storing options of the Bayesian...
xmcmcObject of class XdeMcmc
xsScoresAlternative cross-study scores of differential expression
zeroNuOption for not modeling Nu
XDE documentation built on Nov. 8, 2020, 5:02 p.m.