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XDE (version 2.18.0)

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

Description

Multi-level model for cross-study detection of differential gene expression.

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Version

Version

2.18.0

License

LGPL-2

Maintainer

Robert Scharpf

Last Published

February 15th, 2017

Functions in XDE (2.18.0)

ExpressionSetList-class

A class for containing a list of ExpressionSets
xmcmc

Object of class XdeMcmc
output

Options for storing results of the MCMC chains
empiricalStart

Empirical starting values for the MCMC
tuning

Tuning parameters for Metropolis-Hastings proposals
Parameters-class

Container for XDE parameters
XdeMcmc-class

Class for storing output from the Bayesian model
posteriorAvg

Accessor and replacement methods for posterior averages of differential expression
pairs-methods

pairs function for high-throughput data
updates

Frequency of updating a parameter per MCMC iteration
symbolsInteresting

Useful for changing the look of pairs plots to emphasize concordant or discordant genes
ExpressionSetList-methods

Methods for ExpressionSetList
studyCenter

Center the expression values in a study to zero
iterations

Number of MCMC iterations
geneCenter

Center the expression values for each gene in a study to zero
thin

How often to write MCMC iterations to file
standardizeSamples

Centers the genes at zero and standardizes the samples to have variance 1
firstMcmc

Values for the first MCMC iteration
calculatePosteriorAvg

Calculate the posterior average for indicators of concordant and discordant differential expression
burnin

Indicator for running a MCMC burnin
xde

Fit the Bayesian hierarchical model for cross-study differential gene expression
ssStatistic

Calculate single study estimates of effect size
xsScores

Alternative cross-study scores of differential expression
expressionSetList

Example of ExpressionSetList
seed

Seed for the MCMC
hyperparameters

Accessor for hyperparameters of the Bayesian model
lastMcmc

MCMC values for the last iteration
XdeParameter-class

Container class for storing options of the Bayesian hierarchical model
zeroNu

Option for not modeling Nu