UCSCSession-class {rtracklayer} | R Documentation

## Class "UCSCSession"

### Description

An implementation of `BrowserSession` for the UCSC genome browser.

### Objects from the Class

Objects can be created by calls of the form `browserSession("ucsc", url = "http://genome.ucsc.edu/cgi-bin", ...)`. The arguments in `...` correspond to libcurl options, see `getCurlHandle`. Setting these options may be useful e.g. for getting past a proxy.

### Slots

`url`:

  Object of class `"character"` holding the base URL of the UCSC browser.

`hguid`:

  Object of class `"numeric"` holding the user identification code.

`views`:

  Object of class `"environment"` containing a list stored under the name "instances". The list holds the instances of `BrowserView` for this session.

### Extends

Class `"BrowserSession"`, directly.

### Methods

`browserView(object, range = range(object), track = trackNames(object), ...)`

  Creates a `BrowserView` of `range` with visible tracks specified by `track`. `track` may be an instance of `UCSCTrackModes`. Arguments in `...` should match parameters to a `ucscTrackModes` method for creating a `UCSCTrackModes` instance that will be merged with and override modes indicated by the `track` parameter.

`browserViews`(object)

  Gets the `BrowserView` instances for this session.

`range`(x)

  Gets the `GRanges` last displayed in this session.

`genome(x)`

  Gets the genome identifier of the session, i.e. `genome(range(x))`.

`seqinfo`

  Gets the `Seqinfo` object with the lengths of the chromosomes in the currenet genome. No circularity information is available.

`range(x) <- value`

  Sets `value`, usually a `GRanges` object or `IntegerRangesList`, as the range of session `x`. Note that this setting only lasts until a view is created or manipulated. This mechanism is useful, for example, when treating the UCSC browser as a database, rather than a genome viewer.

`genome(x) <- value`

  Sets the genome identifier on the range of session `x`.

`getSeq(object, range, track = "Assembly")`

  Gets the sequence in `range` and `track`.

`track(object, name = names(track), format = "auto", ...) <- value`

  Loads a track, stored under `name` and formatted as `format`. The "auto" format resolves to "bed" for qualitative data. For quantitative data, i.e., data with a numeric `score` column, "wig" or "bedGraph" is chosen, depending on how well the data compresses into wig. The arguments in `...` are passed on to `export.ucsc`, so they could be slots in a `TrackLine` subclass (and thus specify visual attributes like color) or parameters to pass on to the export function for `format`. The `value` may be either a range object (like a `GRanges`) or a file object (like a `BEDFile`).

`track(object, name, range = range(object), table = NULL)`

  Retrieves a `GRanges` with features in `range` from track named `name`. Some built-in tracks have multiple series, each stored in a separate database table. A specific table may be retrieved by passing its name in the `table` parameter. See `tableNames` for a way to list the available tables.

  `getTable(object, name, range = base::range(object), table = NULL)`: Retrieves the table indicated by the track `name` and `table` name, over `range`, as a `data.frame`. See `getTable`.

`trackNames`(object)

  Gets the names of the tracks stored in the session.

`ucscTrackModes`(object)

  Gets the default view modes for the tracks in the session.

### Author(s)

Michael Lawrence

### See Also

`browserSession` for creating instances of this class.

[Package rtracklayer version 1.49.5 Index]