scoreList-class {tigre} | R Documentation

## Class "scoreList"

### 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")

[Package tigre version 1.38.0 Index]