output: Options for storing results of the MCMC chains
In XDE: XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression

Description Usage Arguments Details Value Note Author(s) See Also Examples

A numeric vector indicating which chains to write to file and, for those parameters that are written to file, how often the chains should be written to file.

1	output(object)

object

An object of class XdeParameter or XdeMcmc

Replacement methods are only available for objects of class XdeParameter. Accessor methods are available for objects of class XdeParameter and XdeMcmc.

A named numerical vector. The first element (thin) specifies how often to write chains to file. For instance, if output[1]=2 the chains will be written to file every other iteration. Elements 2 - 22 of the vector are indicators for whether to write the write the chains of the Bayesian parameters to file.

Parameters indexed by gene and study (Delta, Phi, Nu, and sigma2) grow very large quickly.

R. Scharpf

burnin, XdeParameter-class, XdeMcmc-class

1 2	data(xmcmc) output(xmcmc)

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

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Welcome to XDE version 2.22.0
         thin     potential    acceptance            nu        DDelta 
            2             0             0             0             0 
            a             b            c2        gamma2             r 
            1             1             1             1             1 
          rho         delta            xi        sigma2             t 
            1             0             1             0             1 
            l           phi         theta        lambda         tau2R 
            1             0             1             1             1 
      tau2Rho     probDelta diffExpressed 
            1             0             1