UCSCSession-class: 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 RangesList, 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.