ebarraysFamily-class {EBarrays} | R Documentation |
Objects used as family in the emfit
function.
The package contains two functions that create such objects for the two most commonly used families, Gamma-Gamma and Lognormal-Normal. Users may create their own famiies as well.
eb.createFamilyGG() eb.createFamilyLNN()
The emfit
function can potentially fit models
corresponding to several different Bayesian conjugate families. This
is specified as the family
argument, which ultimately has to be
an object of formal class ``ebarraysFamily'' with some specific slots
that determine the behaviour of the `family'.
For users who are content to use the predefined GG and LNN models, no
further details than that given in the documentation for
emfit
are necessary. If you wish to create your own
families, read on.
Objects of class ``ebarraysFamily'' for the two predefined families Gamma-Gamma and Lognormal-Normal
Objects of class ``ebarraysFamily'' can be created by calls of the
form new("ebarraysFamily", ...)
. Predefined objects
corresponding to the GG and LNN models can be created by
eb.createFamilyGG()
and eb.createFamilyLNN()
. The same
effect is achieved by coercing from the strings "GG"
and
"LNN"
by as("GG", "ebarraysFamily")
and as("LNN",
"ebarraysFamily")
.
An object of class ``ebarraysFamily'' extends the class
"character"
(representing a short hand name for the class) and
should have the following slots (for more details see the source
code):
description
:link
:log(sigma^2)
for LNN). This allows the user to think in terms of familiar
parametrizations that may not necessarily be the best when
optimizing w.r.t. those parameters.
invlink
:thetaInit
:data
(matrix containing raw
expression values), that calculates and returns as a numeric
vector initial estimates of the parameters (in the parametrization
used for optimization)
f0
:theta
and a list called
args
. f0
calculates the negative log likelihood at
the given parameter value theta
(again, in the
parametrization used for optimization). This is called from
emfit
. When called, only genes with positive intensities
across all samples are used.
f0.pp
:f0.pp
is essentially the same as f0
except the terms
common to the numerator and denominator when calculating posterior
odds may be removed. It is called from postprob
.
f0.arglist
:data
and patterns
(of
class ``ebarraysPatterns'') and returns a list with two
components, common.args
and
pattern.args
. common.args
is a list of arguments to
f0
that don't change from one pattern to another, whereas
pattern.args[[i]][[j]]
is a similar list of arguments, but
specific to the columns in pattern[[i]][[j]]
. Eventually,
the two components will be combined for each pattern and used as
the args
argument to f0
.
logDensity
:x
(data vector, containing log
expressions) and theta
(parameters in user-visible
parametrization). Returns log marginal density of the natural log
of intensity for the corresponding theoretical model. Used in
plotMarginal
lower.bound
:theta
of
f0
. Used in optim
upper.bound
:theta
of
f0
.
Christina Kendziorski, Michael Newton and Deepayan Sarkar
show(eb.createFamilyGG()) show(eb.createFamilyLNN())