XdeParameter-class {XDE} | R Documentation |
This class contains initial values for the first iteration of the MCMC, options for saving MCMC chains, options for changing the tuning parameters of the Metropolis-Hastings algorithm, options for changing hyperparameters from their defaults, etc.
Objects can be created by calls of the form new("XdeParameter", esetList, updates, tuning, hyperparameters, output, iterations, burnin, seed, randomSeed, genes, studies, firstMcmc, specifiedInitialValues, directory, phenotypeLabel, showIterations, verbose, studyNames)
.
updates
:numeric
. The frequency
of updates for each iteration of the chain.tuning
:numeric
. Tuning
parameters for the Metropolis-Hastings proposals hyperparameters
:numeric
. Hyperparameters for the Bayesian hierarchical modeloutput
:numeric
. Indicator for
whether to save the MCMC chain to file. If the value is zero, the
chain is not saved.iterations
:numeric
. The total
number of MCMC iterations.burnin
:logical
. If set to
FALSE, by default none of the chains will be saved (called for its
side-effect of setting the output to zero for each parameter).notes
:character
. firstMcmc
:environment
. Values
for the first iteration of the MCMC showIterations
:logical
.
Whether to show the MCMC iteration when fitting the modelspecifiedInitialValues
:logical
. If TRUE (the default), the values stored in
firstMcmc
will be used for the first iteration of the MCMC. directory
:character
. Specifies
where to write the log filesphenotypeLabel
:character
. The
name of the binary covariate used for differential expression verbose
:logical
studyNames
:character
. Names of
the datasetssignature(object = "XdeParameter")
logical.
See burnin
signature(object = "XdeParameter", value =
"logical")
logical. See burnin
signature(object = "XdeParameter")
character
string giving the path or relative path to store log files from the
MCMC chainsignature(object = "XdeParameter")
Path to
store log files. signature(object = "XdeParameter")
See firstMcmc
signature(object = "XdeParameter", value = "environment")
signature(object = "XdeParameter", value = "list")
signature(object = "XdeParameter")
See
the XdeParameterClass vignettesignature(object = "XdeParameter")
See
the XdeParameterClass vignettesignature(.Object = "XdeParameter")
Method
for initializing an instance of the class. The default values
provided work well in most cases.signature(object = "XdeParameter")
Accessor
for the total number of MCMC iterations to runsignature(object = "XdeParameter", value =
numeric)
The replacement method is useful for setting a
different number of iterations.signature(object = "XdeParameter", value = "integer")
signature(object = "XdeParameter")
See also
output
. This method is also defined for class XdeMcmc
signature(object = "XdeParameter")
See also output
signature(object = "XdeParameter")
The name of a binary covariate present in each studysignature(object = "XdeParameter", value = "character")
signature(object = "XdeParameter")
The
number of MCMC iterations written to file. It is the value of the
total number of iterations divided by the thinning parameter. See
also output
signature(object = "XdeParameter")
See
seed
signature(object = "XdeParameter",
value="integer")
Replacement method. See also seed
.signature(object = "XdeParameter")
Produces a
short summary of objects that are instances of the
XdeParameter
classsignature(object = "XdeParameter")
logicalsignature(object = "XdeParameter")
signature(object = "XdeParameter")
Names of
the high-throughput gene expression studiessignature(object = "XdeParameter")
signature(x = "XdeParameter")
See
output
and thin
signature(x = "XdeParameter", value = numeric)
See thin
signature(object = "XdeParameter")
See also tuning
signature(object = "XdeParameter")
signature(object = "XdeParameter")
See also updates
signature(object = "XdeParameter")
R. Scharpf
R. Scharpf
showClass("XdeParameter") ##See the XdeParameterClass vignette