Infrastructure to to store and process MCMC results

The bandleParams infrastructure is used to store and process MCMC results for bandle model from Crook et al 2021

chains(object)

# S4 method for bandleParams
show(object)

# S4 method for nicheParam
show(object)

# S4 method for bandleChain
show(object)

# S4 method for bandleChains
length(x)

# S4 method for bandleParams
length(x)

# S4 method for bandleSummaries
length(x)

# S4 method for nicheParams
length(x)

# S4 method for nicheParams
length(x)

posteriorEstimates(object)

# S4 method for bandleSummary
posteriorEstimates(object)

summaries(object)

params(object)

bandleJoint(object)

# S4 method for bandleSummary
bandleJoint(object)

# S4 method for bandleChains,ANY,ANY
[[(x, i, j = "missing", drop = "missing")

# S4 method for bandleParams,ANY,ANY
[[(x, i, j = "missing", drop = "missing")

# S4 method for bandleChains,ANY,ANY,ANY
[(x, i, j = "missing", drop = "missing")

# S4 method for bandleParams,ANY,ANY,ANY
[(x, i, j = "missing", drop = "missing")

# S4 method for bandleChains
show(object)

# S4 method for bandleSummaries
show(object)

# S4 method for bandleSummaries,ANY,ANY
[[(x, i, j = "missing", drop = "missing")

# S4 method for bandleSummaries,ANY,ANY
[[(x, i, j = "missing", drop = "missing")

# S4 method for bandleSummaries,ANY,ANY,ANY
[(x, i, j = "missing", drop = "missing")

# S4 method for nicheParams,ANY,ANY
[[(x, i, j = "missing", drop = "missing")

# S4 method for nicheParams,ANY,ANY
[[(x, i, j = "missing", drop = "missing")

# S4 method for nicheParams,ANY,ANY,ANY
[(x, i, j = "missing", drop = "missing")

# S4 method for nicheParams
show(object)

Arguments

object: object of class nicheParams.
x: Object to be subset.
i: An integer(). Should be of length 1 for [[.
j: Missing.
drop: Missing.

Value

An object of class bandleParams which stores the main results for the analysis when using bandle

Details

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

Slots

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.