Man pages for XDE
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
| burnin | Indicator for running a MCMC burnin |
| calculatePosteriorAvg | Calculate the posterior average for indicators of concordant... |
| empiricalStart | Empirical starting values for the MCMC |
| expressionSetList | Example of ExpressionSetList |
| ExpressionSetList-class | A class for containing a list of ExpressionSets |
| ExpressionSetList-methods | Methods for ExpressionSetList |
| firstMcmc | Values for the first MCMC iteration |
| geneCenter | Center the expression values for each gene in a study to zero |
| hyperparameters | Accessor for hyperparameters of the Bayesian model |
| iterations | Number of MCMC iterations |
| lastMcmc | MCMC values for the last iteration |
| output | Options for storing results of the MCMC chains |
| pairs | pairs function for high-throughput data |
| Parameters-class | Container for XDE parameters |
| posteriorAvg | Accessor and replacement methods for posterior averages of... |
| seed | Seed for the MCMC |
| ssStatistic | Calculate single study estimates of effect size |
| standardizeSamples | Centers the genes at zero and standardizes the samples to... |
| studyCenter | Center the expression values in a study to zero |
| symbolsInteresting | Useful for changing the look of pairs plots to emphasize... |
| thin | How often to write MCMC iterations to file |
| tuning | Tuning parameters for Metropolis-Hastings proposals |
| updates | Frequency of updating a parameter per MCMC iteration |
| xde | Fit the Bayesian hierarchical model for cross-study... |
| XdeMcmc-class | Class for storing output from the Bayesian model |
| XdeParameter-class | Container class for storing options of the Bayesian... |
| xmcmc | Object of class XdeMcmc |
| xsScores | Alternative cross-study scores of differential expression |
| zeroNu | Option for not modeling Nu |
