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 = "https://genome.ucsc.edu/cgi-bin", ...). The arguments in ... correspond to libcurl options, see httr_options. 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.