enrichment {SNPhood} | R Documentation

## Extract enrichment data from an object.

### Description

Extract enrichment data from an object.

`enrichment` extracts enrichment data from a `SNPhood` object. The full count data or only a subset can be extracted by settings the parameters `type`, `readGroup` and `dataset` accordingly. Principally, either the count data for the unbinned or binned SNP regions can be extracted.

### Usage

    enrichment(object, ...)

    ## S4 method for signature 'SNPhood'
    enrichment(object, readGroup = NULL, dataset = NULL,
      ...)

### Arguments

`object` | An object containing enrichment information.
`...` | Additional arguments, for use in specific methods.
`readGroup` | Character(1). Default NULL. Read group that should be plotted, specified by its name as obtained by the function `annotationReadGroups`). If only one read group is defined in the object, this may also be NULL for user conveniance.
`dataset` | Numeric(1) or Character(1). Single dataset that should be used for plotting, either specified as integer (such as 1, value must be between 1 and the total number of datasets as defined in the object) or its annotation (name must appear in the dataset names as obtained via the function `annotationDatasets`).

### Value

Enrichment of the object or the objects components.

Named list with the requested enrichment matrices from the `SNPhood` object, organized by read group and dataset

### See Also

`counts`

### Examples

    data(SNPhood.o, package="SNPhood")
    str(enrichment(SNPhood.o), list.len=5)

[Package SNPhood version 1.12.0 Index]