Parameters-class: Container for XDE parameters

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

Description

Container for XDE parameters

Objects from the Class

Objects can be created by calls of the form new("Parameters", ...).

Slots

seed:

Object of class "integer" ~~

data:

Object of class "numeric" ~~

phenodata:

Object of class "integer" ~~

G:

Object of class "integer" ~~

Q:

Object of class "integer" ~~

S:

Object of class "integer" ~~

alphaA:

Object of class "numeric" ~~

alphaB:

Object of class "numeric" ~~

betaA:

Object of class "numeric" ~~

betaB:

Object of class "numeric" ~~

pA0:

Object of class "numeric" ~~

pA1:

Object of class "numeric" ~~

pB0:

Object of class "numeric" ~~

pB1:

Object of class "numeric" ~~

nuR:

Object of class "numeric" ~~

nuRho:

Object of class "numeric" ~~

alphaXi:

Object of class "numeric" ~~

betaXi:

Object of class "numeric" ~~

c2Max:

Object of class "numeric" ~~

alphaEta:

Object of class "numeric" ~~

betaEta:

Object of class "numeric" ~~

pOmega0:

Object of class "numeric" ~~

lambdaOmega:

Object of class "numeric" ~~

lambdaKappa:

Object of class "numeric" ~~

gamma2:

Object of class "numeric" ~~

c2:

Object of class "numeric" ~~

tau2Rho:

Object of class "numeric" ~~

tau2R:

Object of class "numeric" ~~

a:

Object of class "numeric" ~~

b:

Object of class "numeric" ~~

l:

Object of class "numeric" ~~

t:

Object of class "numeric" ~~

lambda:

Object of class "numeric" ~~

theta:

Object of class "numeric" ~~

phi:

Object of class "numeric" ~~

sigma2:

Object of class "numeric" ~~

r:

Object of class "numeric" ~~

rho:

Object of class "numeric" ~~

nu:

Object of class "numeric" ~~

delta:

Object of class "numeric" ~~

Delta:

Object of class "numeric" ~~

xi:

Object of class "numeric" ~~

Methods

"[[<-"

signature(x = "Parameters"): ...

"[["

signature(x = "Parameters"): ...

"$<-"

signature(x = "Parameters"): ...

$

signature(x = "Parameters"): ...

coerce

signature(from = "XdeParameter", to = "Parameters"): ...

show

signature(object = "Parameters"): ...

Examples

showClass("Parameters")

Example output

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

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 2.22.0
Class "Parameters" [package "XDE"]

Slots:
                                                                              
Name:         seed        data   phenodata           G           Q           S
Class:     integer     numeric     integer     integer     integer     integer
                                                                              
Name:       alphaA      alphaB       betaA       betaB         pA0         pA1
Class:     numeric     numeric     numeric     numeric     numeric     numeric
                                                                              
Name:          pB0         pB1         nuR       nuRho     alphaXi      betaXi
Class:     numeric     numeric     numeric     numeric     numeric     numeric
                                                                              
Name:        c2Max    alphaEta     betaEta     pOmega0 lambdaOmega lambdaKappa
Class:     numeric     numeric     numeric     numeric     numeric     numeric
                                                                              
Name:       gamma2          c2     tau2Rho       tau2R           a           b
Class:     numeric     numeric     numeric     numeric     numeric     numeric
                                                                              
Name:            l           t      lambda       theta         phi      sigma2
Class:     numeric     numeric     numeric     numeric     numeric     numeric
                                                                              
Name:            r         rho          nu       delta       Delta          xi
Class:     numeric     numeric     numeric     numeric     numeric     numeric

Known Subclasses: 
Class "ParametersD", directly
Class "ParametersMII", directly
Class "ParametersC", by class "ParametersD", distance 2

XDE documentation built on Nov. 8, 2020, 5:02 p.m.