selectTop {baySeq} | R Documentation

## Selects the top genomic events, based on posterior likelihoods, from a ‘countData’ object.

### Description

This function subsets a countData object by selecting those events that best (or least) represent a model, based on the posterior likelihoods estimated for that model and some threshold. Selection can be done for a specific model (and ordering of the data under that model) or for all models (and all orderings).

### Usage

    selectTop(cD, group, ordering, orderings = TRUE, decreasing = TRUE,
    number = 10, likelihood, FDR, FWER, posteriors)

### Arguments

`cD` | A `countData` object, with a populated ‘@posteriors’ slot (unless ‘posteriors’ is specified; see below).
`group` | Optionally, the model of interest, as defined in the ‘@groups’ slot of the `countData` object. If unspecified, subsets for all models will be returned as a list.
`ordering` | If ‘group’ is specified, a particular ordering of the data based on that group can also be specified.
`orderings` | If no group is specified, should the selection of models also be split by the orderings of the data under the models? Defaults to TRUE.
`decreasing` | If FALSE, considers the data with the lowest posterior likelihoods, rather than the greatest (i.e., selects those data least likely to conform to a particular model.
`number` | If given, selects the top 'number' of genomic events for each model (and optionally, ordering). Ignored if another selection criteria is chosen, unless this criteria would return no values.
`likelihood` | If given, selects all genomic events for a given model (and optionally, ordering) with posterior likelihood exceeding this value.
`FDR` | If given, selects all genomic events for a given model (and optionally, ordering) with false discovery rate below this value. Ignored if likelihood is specified.
`FWER` | If given, selects all genomic events for a given model (and optionally, ordering) with family-wise error rate below this value. Ignored if likelihood or FDR is specified.
`posteriors` | If given, a vector of log-posterior likelihoods to use instead of those in the ‘@posteriors’ slot of the ‘cD’ object.

### Value

Either a single `countData` object (if ‘group’ is specified), or a named list of `countData` objects.

### Author(s)

Thomas J. Hardcastle

### See Also

`topCounts`

### Examples

    # We load in a `countData' object containing the estimated posterior
    # likelihoods of expression (see `getLikelihoods').

    data(CDPost)

    # select from all models and orderings with FDR equal to or lower than 0.01.

    selectTop(CDPost, FDR = 0.01)

[Package baySeq version 2.20.0 Index]