bandleChains-class | R Documentation |
The bandleParams
infrastructure is used to store and process MCMC results for
bandle model from Crook et al 2021
chains(object) ## S4 method for signature 'bandleParams' show(object) ## S4 method for signature 'nicheParam' show(object) ## S4 method for signature 'bandleChain' show(object) ## S4 method for signature 'bandleChains' length(x) ## S4 method for signature 'bandleParams' length(x) ## S4 method for signature 'bandleSummaries' length(x) ## S4 method for signature 'nicheParams' length(x) ## S4 method for signature 'nicheParams' length(x) posteriorEstimates(object) ## S4 method for signature 'bandleSummary' posteriorEstimates(object) summaries(object) params(object) bandleJoint(object) ## S4 method for signature 'bandleSummary' bandleJoint(object) ## S4 method for signature 'bandleChains,ANY,ANY' x[[i, j = "missing", drop = "missing"]] ## S4 method for signature 'bandleParams,ANY,ANY' x[[i, j = "missing", drop = "missing"]] ## S4 method for signature 'bandleChains,ANY,ANY,ANY' x[i, j = "missing", drop = "missing"] ## S4 method for signature 'bandleParams,ANY,ANY,ANY' x[i, j = "missing", drop = "missing"] ## S4 method for signature 'bandleChains' show(object) ## S4 method for signature 'bandleSummaries' show(object) ## S4 method for signature 'bandleSummaries,ANY,ANY' x[[i, j = "missing", drop = "missing"]] ## S4 method for signature 'bandleSummaries,ANY,ANY' x[[i, j = "missing", drop = "missing"]] ## S4 method for signature 'bandleSummaries,ANY,ANY,ANY' x[i, j = "missing", drop = "missing"] ## S4 method for signature 'nicheParams,ANY,ANY' x[[i, j = "missing", drop = "missing"]] ## S4 method for signature 'nicheParams,ANY,ANY' x[[i, j = "missing", drop = "missing"]] ## S4 method for signature 'nicheParams,ANY,ANY,ANY' x[i, j = "missing", drop = "missing"] ## S4 method for signature 'nicheParams' show(object)
object |
object of class nicheParams. |
x |
Object to be subset. |
i |
An |
j |
Missing. |
drop |
Missing. |
Objects of the bandleParams
class are created with the bandle()
function
These objects store the priors for the model and the results of the MCMC
chains, which themselves are stored as an instance of class bandleChains
and
can be accessed with the chains()
function. A summary of the bandleChains
(or class bandleSummary
) can be further computed with the bandleProcess
function.
see the bandle vignette for examples
An object of class bandleParams
which stores the main results
for the analysis when using bandle
chains
list()
containing the individual full MCMC chain
results in an bandleChains
instance. Each element must be a
valid bandleChain
instance.
posteriorEstimates
A DataFrame
documenting the posteriors
in an bandleSummary
instance
diagnostics
A matrix
of dimensions 1 by 2 containing the
bandleSummary
diagnostics.
bandle.joint
A matrix
of dimensions N by K storing the joint
probability in an bandleSummary
instance for each of the first condition
chains
list()
containing the individual bandle Summaries for
different conditions results in an bandleSummaries
instance. Each element must be a
valid bandleSummary
instance.
method
A character()
storing the bandle method name
priors
A list()
with the priors for the parameters
seed
An integer()
with the random number generation seed.
summary
Object of class bandleSummary
the summarised MCMC results
available in the bandleParams
instance.
chains
Object of class bandleChains
containing the full MCMC results
in the bandleParams
instance
datset
character
indicating which dataset i.e control or treatment
replicate
integer
an integer indicating which replicate
K
integer(1)
indicating the number of components.
D
integer(1)
indicating the number of samples.
method
character(1)
defining the method used. Currently
bandle
mk
matrix(K, D)
lambdak
numeric(K)
nuk
numeric(K)
sk
array(K, D, D)
params
list()
containing the individual nicheParam
objects
results in an bandleParams
instance. Each element must be a
valid bandleParam
instance.
dataset
character
indicating the dataset usaully control or treatment
replicate
integer
indicating the number of dataset replicate
n
integer(1)
indicating the number of MCMC interactions.
Stored in an bandleChain
instance.
K
integer(1)
indicating the number of components. Stored
in an bandleChain
instance.
N
integer(1)
indicating the number of proteins. Stored in
an bandleChain
instance.
niche
matrix(N, n)
component allocation results of an
bandleChain
instance.
nicheProb
matrix(N, n, K)
component allocation
probabilities of an bandleChain
instance.
outlier
matrix(N, n)
outlier allocation results.
outlierProb
matrix(N, n, 2)
outlier allocation
probabilities of an bandleChain
instance.
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