Object of class XdeMcmc

Description

An object of class XdeMcmc is created by fitting the Bayesian hierarchical model to the expressionSetList example data.

Usage

data(xmcmc)

Details

The xmcmc data example was obtained as described in the XDE vignette.

Examples

data(xmcmc)
xmcmc

##ordinarily, one should not need to change the directory in an object
##of class XdeMcmc -- therefore, a replacment method is not defined
pathToLogFiles <- system.file("logFiles", package="XDE")
xmcmc@directory <- pathToLogFiles

##The $ operator can be used to extract chains. For instance, here we
##extract the c2 chain
c2 <- xmcmc$c2
plot.ts(c2)

Results

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> library(XDE)
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Welcome to XDE version 2.18.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/XDE/xmcmc.Rd_%03d_medium.png", width=480, height=480)
> ### Name: xmcmc
> ### Title: Object of class XdeMcmc
> ### Aliases: xmcmc
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(xmcmc)
> xmcmc
Instance of XdeMcmc 
Study names: split1 split2 split3 
Number of features: 500 

seed (a new seed): -1668623711 

iterations (saved): 1000 

output (parameters saved):
    potential    acceptance            nu        DDelta             a 
        FALSE         FALSE         FALSE         FALSE          TRUE 
            b            c2        gamma2             r           rho 
         TRUE          TRUE          TRUE          TRUE          TRUE 
        delta            xi        sigma2             t             l 
        FALSE          TRUE         FALSE          TRUE          TRUE 
          phi         theta        lambda         tau2R       tau2Rho 
        FALSE          TRUE          TRUE          TRUE          TRUE 
    probDelta diffExpressed 
        FALSE          TRUE 

directory (of saved log files): logFiles/ 

lastMcmc: environment 

posteriorAvg: NULL
bayesianEffectSize: NULL
> 
> ##ordinarily, one should not need to change the directory in an object
> ##of class XdeMcmc -- therefore, a replacment method is not defined
> pathToLogFiles <- system.file("logFiles", package="XDE")
> xmcmc@directory <- pathToLogFiles
> 
> ##The $ operator can be used to extract chains. For instance, here we
> ##extract the c2 chain
> c2 <- xmcmc$c2
Read 1000 items
> plot.ts(c2)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>