scoreList-class: Class "scoreList"

In ahonkela/tigre: Transcription factor Inference through Gaussian process Reconstruction of Expression

Description

'scoreList' is an object which contain the genes, parameters, log-likelihoods and arguments of models. With the data in a scoreList item and the original data used for creating the models, the models can be reconstructed with the function 'generateModels'.

Objects from the Class

Objects can be created by calls of the form scoreList(params, loglikelihoods, genes, modelArgs, knownTargets, TF, sharedModel).

Slots

params:

The parameters of the models.

loglikelihoods:

The log-likelihoods of the models.

baseloglikelihoods:

The log-likelihoods of corresponding null models.

genes:

The genes used in the models.

modelArgs:

A list of arguments used to generate the models.

knownTargets:

The list of known targets used in the ranking.

TF:

The TF used in the ranking.

sharedModel:

Shared model for known targets.

datasetName:

Dataset name, used when exporting scores to a database.

experimentSet:

Experiment set name, used when exporting scores to a database.

Methods

Class-specific methods:

write.scores(object, ...)

Writes the log-likelihoods and null log-likelihoods. Accepts any options write.table does.

genes(object), genes(object)<- value

Access and set genes

knownTargets(object), knownTargets(object)<- value

Access and set knownTargets

loglikelihoods(object), loglikelihoods(object)<- value

Access and set loglikelihoods

baseloglikelihoods(object), baseloglikelihoods(object)<- value

Access and set baseloglikelihoods

modelArgs(object), modelArgs(object)<- value

Access and set modelArgs

params(object), params(object)<- value

Access and set params

sharedModel(object), sharedModel(object)<- value

Access and set sharedModel

TF(object), TF(object)<- value

Access and set TF

datasetName(object), datasetName(object)<- value

Access and set datasetName

experimentSet(object), experimentSet(object)<- value

Access and set experimentSet

Standard generic methods:

object[(index)

Conducts subsetting of the scoreList.

c(object, ...)

Concatenates scoreLists.

length(object)

Returns the length of the list.

show(object)

Informatively display object contents.

sort(object, decreasing=FALSE)

Sort the list according to log-likelihood

Author(s)

Antti Honkela, Jonatan Ropponen

See Also

GPRankTargets, GPRankTFs, generateModels, write.table.

Examples

showClass("scoreList")

ahonkela/tigre documentation built on Aug. 6, 2021, 12:08 p.m.